From 29741aa2c1d7195a49f06a4b5f2f9ad01f7c28d2 Mon Sep 17 00:00:00 2001 From: Peter van Heusden Date: Mon, 15 Nov 2021 14:29:35 +0000 Subject: [PATCH 01/36] Add support for running IRIDA with Galaxy --- compose/docker-compose.irida.yml | 61 ++ compose/docker-compose.yml | 5 + compose/extra-tools.yml | 7 + compose/galaxy-configurator/Dockerfile | 2 +- compose/galaxy-configurator/run.sh | 26 +- .../templates/galaxy/job_conf.xml.j2 | 2 +- .../templates/galaxy/tool_sheds_conf.xml.j2 | 7 + .../templates/irida/irida.conf.j2 | 145 +++ ...2-artic-illumina-pipeline-plugin-0.1.9.jar | Bin 0 -> 103168 bytes ...2-artic-nanopore-pipeline-plugin-0.1.3.jar | Bin 0 -> 17882 bytes ...2-artic-nanopore-pipeline-plugin-0.1.4.jar | Bin 0 -> 24560 bytes .../irida/static/css/bootstrap.min.css | 7 + .../irida/static/logos/NRF_logo_small.png | Bin 0 -> 17444 bytes .../irida/static/logos/SAMRCnewLogo.png | Bin 0 -> 9596 bytes .../irida/static/logos/SANBI_logo_small.png | Bin 0 -> 10376 bytes .../irida/static/logos/UWC_logo_small.png | Bin 0 -> 39759 bytes .../static/logos/combat_tb_logo_small.png | Bin 0 -> 2510 bytes .../irida/static/logos/dsi_logo_small.png | Bin 0 -> 52747 bytes .../templates/irida/templates/login.html | 75 ++ .../templates/irida/web.conf.j2 | 24 + .../templates/nginx/nginx.conf.j2 | 21 + compose/galaxy-server/Dockerfile | 8 +- compose/galaxy-server/files/start.sh | 6 +- compose/irida/Dockerfile | 67 ++ compose/irida/docker-entrypoint.sh | 26 + .../etc-irida/static/css/bootstrap.min.css | 7 + .../etc-irida/static/logos/NRF_logo_small.png | Bin 0 -> 17444 bytes .../etc-irida/static/logos/SAMRCnewLogo.png | Bin 0 -> 9596 bytes .../static/logos/SANBI_logo_small.png | Bin 0 -> 10376 bytes .../etc-irida/static/logos/UWC_logo_small.png | Bin 0 -> 39759 bytes .../static/logos/combat_tb_logo_small.png | Bin 0 -> 2510 bytes .../etc-irida/static/logos/dsi_logo_small.png | Bin 0 -> 52747 bytes compose/irida/etc-irida/templates/login.html | 75 ++ compose/irida/galaxy_tools.yml | 82 ++ compose/irida/irida.conf | 142 +++ compose/irida/nginx-config | 19 + compose/irida/start-daemons.sh | 3 + compose/irida/tmp/META-INF/MANIFEST.MF | 12 + compose/irida/tmp/META-INF/extensions.idx | 2 + .../pom.properties | 4 + .../pom.xml | 96 ++ .../ArticIlluminaPlugin$PluginInfo.class | Bin 0 -> 3026 bytes .../irida/plugins/ArticIlluminaPlugin.class | Bin 0 -> 921 bytes .../plugins/ArticIlluminaPluginUpdater.class | Bin 0 -> 14104 bytes .../irida/plugins/MetadataValue.class | Bin 0 -> 525 bytes .../irida/plugins/QCReport.class | Bin 0 -> 590 bytes .../tmp/workflows/0.1.0/irida_workflow.xml | 262 +++++ .../0.1.0/irida_workflow_structure.ga | 714 ++++++++++++++ .../workflows/0.1.0/messages_en.properties | 86 ++ .../tmp/workflows/0.1.1/irida_workflow.xml | 294 ++++++ .../0.1.1/irida_workflow_structure.ga | 815 ++++++++++++++++ .../workflows/0.1.1/messages_en.properties | 95 ++ .../tmp/workflows/0.1.2/irida_workflow.xml | 294 ++++++ .../0.1.2/irida_workflow_structure.ga | 815 ++++++++++++++++ .../workflows/0.1.2/messages_en.properties | 95 ++ .../tmp/workflows/0.1.3/irida_workflow.xml | 294 ++++++ .../0.1.3/irida_workflow_structure.ga | 815 ++++++++++++++++ .../workflows/0.1.3/messages_en.properties | 95 ++ .../tmp/workflows/0.1.4/irida_workflow.xml | 293 ++++++ .../0.1.4/irida_workflow_structure.ga | 822 ++++++++++++++++ .../workflows/0.1.4/messages_en.properties | 95 ++ .../tmp/workflows/0.1.5/irida_workflow.xml | 294 ++++++ .../0.1.5/irida_workflow_structure.ga | 815 ++++++++++++++++ .../workflows/0.1.5/messages_en.properties | 90 ++ .../tmp/workflows/0.1.6/irida_workflow.xml | 295 ++++++ .../0.1.6/irida_workflow_structure.ga | 840 ++++++++++++++++ .../workflows/0.1.6/messages_en.properties | 90 ++ .../tmp/workflows/0.1.7/irida_workflow.xml | 278 ++++++ .../0.1.7/irida_workflow_structure.ga | 909 ++++++++++++++++++ .../workflows/0.1.7/messages_en.properties | 92 ++ .../tmp/workflows/0.1.9/irida_workflow.xml | 128 +++ .../0.1.9/irida_workflow_structure.ga | 904 +++++++++++++++++ .../workflows/0.1.9/messages_en.properties | 97 ++ compose/irida/tmp/workflows/0.1.9/tools.yaml | 83 ++ compose/irida/wait-for-it.sh | 177 ++++ compose/irida/web.conf | 24 + ...2-artic-illumina-pipeline-plugin-0.1.9.jar | Bin 0 -> 103168 bytes ...2-artic-nanopore-pipeline-plugin-0.1.3.jar | Bin 0 -> 17882 bytes 78 files changed, 11921 insertions(+), 10 deletions(-) create mode 100644 compose/docker-compose.irida.yml create mode 100644 compose/extra-tools.yml create mode 100644 compose/galaxy-configurator/templates/galaxy/tool_sheds_conf.xml.j2 create mode 100644 compose/galaxy-configurator/templates/irida/irida.conf.j2 create mode 100644 compose/galaxy-configurator/templates/irida/plugins/sarscov2-artic-illumina-pipeline-plugin-0.1.9.jar create mode 100644 compose/galaxy-configurator/templates/irida/plugins/sarscov2-artic-nanopore-pipeline-plugin-0.1.3.jar create mode 100644 compose/galaxy-configurator/templates/irida/plugins/sarscov2-artic-nanopore-pipeline-plugin-0.1.4.jar create mode 100644 compose/galaxy-configurator/templates/irida/static/css/bootstrap.min.css create mode 100644 compose/galaxy-configurator/templates/irida/static/logos/NRF_logo_small.png create mode 100644 compose/galaxy-configurator/templates/irida/static/logos/SAMRCnewLogo.png create mode 100644 compose/galaxy-configurator/templates/irida/static/logos/SANBI_logo_small.png create mode 100644 compose/galaxy-configurator/templates/irida/static/logos/UWC_logo_small.png create mode 100644 compose/galaxy-configurator/templates/irida/static/logos/combat_tb_logo_small.png create mode 100644 compose/galaxy-configurator/templates/irida/static/logos/dsi_logo_small.png create mode 100644 compose/galaxy-configurator/templates/irida/templates/login.html create mode 100644 compose/galaxy-configurator/templates/irida/web.conf.j2 create mode 100644 compose/irida/Dockerfile create mode 100755 compose/irida/docker-entrypoint.sh create mode 100644 compose/irida/etc-irida/static/css/bootstrap.min.css create mode 100644 compose/irida/etc-irida/static/logos/NRF_logo_small.png create mode 100644 compose/irida/etc-irida/static/logos/SAMRCnewLogo.png create mode 100644 compose/irida/etc-irida/static/logos/SANBI_logo_small.png create mode 100644 compose/irida/etc-irida/static/logos/UWC_logo_small.png create mode 100644 compose/irida/etc-irida/static/logos/combat_tb_logo_small.png create mode 100644 compose/irida/etc-irida/static/logos/dsi_logo_small.png create mode 100644 compose/irida/etc-irida/templates/login.html create mode 100644 compose/irida/galaxy_tools.yml create mode 100644 compose/irida/irida.conf create mode 100644 compose/irida/nginx-config create mode 100644 compose/irida/start-daemons.sh create mode 100644 compose/irida/tmp/META-INF/MANIFEST.MF create mode 100644 compose/irida/tmp/META-INF/extensions.idx create mode 100644 compose/irida/tmp/META-INF/maven/ca.corefacility.bioinformatics.irida.plugins/sarscov2-artic-illumina-pipeline-plugin/pom.properties create mode 100644 compose/irida/tmp/META-INF/maven/ca.corefacility.bioinformatics.irida.plugins/sarscov2-artic-illumina-pipeline-plugin/pom.xml create mode 100644 compose/irida/tmp/ca/corefacility/bioinformatics/irida/plugins/ArticIlluminaPlugin$PluginInfo.class create mode 100644 compose/irida/tmp/ca/corefacility/bioinformatics/irida/plugins/ArticIlluminaPlugin.class create mode 100644 compose/irida/tmp/ca/corefacility/bioinformatics/irida/plugins/ArticIlluminaPluginUpdater.class create mode 100644 compose/irida/tmp/ca/corefacility/bioinformatics/irida/plugins/MetadataValue.class create mode 100644 compose/irida/tmp/ca/corefacility/bioinformatics/irida/plugins/QCReport.class create mode 100644 compose/irida/tmp/workflows/0.1.0/irida_workflow.xml create mode 100644 compose/irida/tmp/workflows/0.1.0/irida_workflow_structure.ga create mode 100644 compose/irida/tmp/workflows/0.1.0/messages_en.properties create mode 100644 compose/irida/tmp/workflows/0.1.1/irida_workflow.xml create mode 100644 compose/irida/tmp/workflows/0.1.1/irida_workflow_structure.ga create mode 100644 compose/irida/tmp/workflows/0.1.1/messages_en.properties create mode 100644 compose/irida/tmp/workflows/0.1.2/irida_workflow.xml create mode 100644 compose/irida/tmp/workflows/0.1.2/irida_workflow_structure.ga create mode 100644 compose/irida/tmp/workflows/0.1.2/messages_en.properties create mode 100644 compose/irida/tmp/workflows/0.1.3/irida_workflow.xml create mode 100644 compose/irida/tmp/workflows/0.1.3/irida_workflow_structure.ga create mode 100644 compose/irida/tmp/workflows/0.1.3/messages_en.properties create mode 100644 compose/irida/tmp/workflows/0.1.4/irida_workflow.xml create mode 100644 compose/irida/tmp/workflows/0.1.4/irida_workflow_structure.ga create mode 100644 compose/irida/tmp/workflows/0.1.4/messages_en.properties create mode 100644 compose/irida/tmp/workflows/0.1.5/irida_workflow.xml create mode 100644 compose/irida/tmp/workflows/0.1.5/irida_workflow_structure.ga create mode 100644 compose/irida/tmp/workflows/0.1.5/messages_en.properties create mode 100644 compose/irida/tmp/workflows/0.1.6/irida_workflow.xml create mode 100644 compose/irida/tmp/workflows/0.1.6/irida_workflow_structure.ga create mode 100644 compose/irida/tmp/workflows/0.1.6/messages_en.properties create mode 100644 compose/irida/tmp/workflows/0.1.7/irida_workflow.xml create mode 100644 compose/irida/tmp/workflows/0.1.7/irida_workflow_structure.ga create mode 100644 compose/irida/tmp/workflows/0.1.7/messages_en.properties create mode 100644 compose/irida/tmp/workflows/0.1.9/irida_workflow.xml create mode 100644 compose/irida/tmp/workflows/0.1.9/irida_workflow_structure.ga create mode 100644 compose/irida/tmp/workflows/0.1.9/messages_en.properties create mode 100644 compose/irida/tmp/workflows/0.1.9/tools.yaml create mode 100755 compose/irida/wait-for-it.sh create mode 100644 compose/irida/web.conf create mode 100644 compose/irida/workflows/sarscov2-artic-illumina-pipeline-plugin-0.1.9.jar create mode 100644 compose/irida/workflows/sarscov2-artic-nanopore-pipeline-plugin-0.1.3.jar diff --git a/compose/docker-compose.irida.yml b/compose/docker-compose.irida.yml new file mode 100644 index 000000000..f210c4fca --- /dev/null +++ b/compose/docker-compose.irida.yml @@ -0,0 +1,61 @@ +# Extend Galaxy to use Singularity for dependency resolution. +# This is working with the base Galaxy, but also in combination +# with different job runners, like HTCondor, or Slurm +# (Pulsar is still WIP). +# Examples: +# * `docker-compose -f docker-compose.yml -f docker-compose.singularity.yml up` +# * `docker-compose -f docker-compose.yml -f docker-compose.slurm.yml -f docker-compose.singularity.yml up` +version: "3.7" +services: + galaxy-server: + environment: + - GALAXY_EXTRA_GROUP=root + - GALAXY_URL=http://nginx:90/ + volumes: + - irida_web_data:/data/irida + galaxy-configurator: + environment: + - GALAXY_SINGULARITY_VOLUMES=/data/irida:rw + - GALAXY_CONFIG_ALLOW_PATH_PASTE=true + - IRIDA_OVERWRITE_CONFIG=true + - IRIDA_CONF_DIR=/etc/irida + - IRIDA_ENABLED=true + volumes: + - ${EXPORT_DIR:-./export}/irida:/etc/irida + nginx: + ports: + - 90:90 + irida-web: + build: irida + container_name: irida-web + depends_on: + - irida-mysql + ports: + - "8080:8080" + volumes: + - ${EXPORT_DIR:-./export}/irida:/etc/irida + - irida_web_data:/data/irida + networks: + - galaxy + + irida-mysql: + restart: always + image: mariadb:10.5.6 + container_name: irida-mysql + environment: + MYSQL_ROOT_PASSWORD: rootpasswd + MYSQL_DATABASE: irida_db + MYSQL_USER: irida_user + MYSQL_PASSWORD: irida_passwd + volumes: + - irida_mysql_data:/var/lib/mysql + ports: + - "33060:3306" + networks: + - galaxy + +volumes: + irida_mysql_data: + irida_web_data: + irida_galaxy_data: + diff --git a/compose/docker-compose.yml b/compose/docker-compose.yml index b1246757a..1bf0086f6 100644 --- a/compose/docker-compose.yml +++ b/compose/docker-compose.yml @@ -30,6 +30,7 @@ services: environment: - EXPORT_DIR=${EXPORT_DIR:-./export} - HOST_PWD=$PWD + - GALAXY_CONF_DIR=/galaxy/config - GALAXY_OVERWRITE_CONFIG=true - GALAXY_DEPENDENCY_RESOLUTION=conda - GALAXY_JOB_RUNNER=local @@ -40,6 +41,7 @@ services: - GALAXY_CONFIG_AMQP_INTERNAL_CONNECTION=amqp://galaxy:vaiJa3ieghai2ief0jao@rabbitmq/galaxy - GALAXY_PROXY_PREFIX=${GALAXY_PROXY_PREFIX:-} - GALAXY_CONFIG_CLEANUP_JOB=onsuccess + - GALAXY_ENABLE_TESTTOOLSHED=true - NGINX_OVERWRITE_CONFIG=true volumes: - ${EXPORT_DIR:-./export}/galaxy/config:/galaxy/config @@ -89,3 +91,6 @@ services: - galaxy networks: galaxy: + driver: bridge + driver_opts: + com.docker.network.driver.mtu: 1450 diff --git a/compose/extra-tools.yml b/compose/extra-tools.yml new file mode 100644 index 000000000..a0677683d --- /dev/null +++ b/compose/extra-tools.yml @@ -0,0 +1,7 @@ +tools: + - name: "data_manager_primer_scheme_bedfiles" + owner: "iuc" + tool_shed_url: "toolshed.g2.bx.psu.edu" + revisions: + - "157a5c9ea72a" + tool_panel_section_label: "COMBAT-SARS-COV-2::ARTIC-MINION" diff --git a/compose/galaxy-configurator/Dockerfile b/compose/galaxy-configurator/Dockerfile index 8efa5611c..c7c028d6a 100644 --- a/compose/galaxy-configurator/Dockerfile +++ b/compose/galaxy-configurator/Dockerfile @@ -1,6 +1,6 @@ FROM alpine:3.11 -RUN apk add --no-cache bash python3 \ +RUN apk add --no-cache bash python3 rsync \ && pip3 install j2cli[yaml] jinja2-ansible-filters COPY ./templates /templates diff --git a/compose/galaxy-configurator/run.sh b/compose/galaxy-configurator/run.sh index fd37d78a5..c7d7c7362 100755 --- a/compose/galaxy-configurator/run.sh +++ b/compose/galaxy-configurator/run.sh @@ -6,10 +6,11 @@ export GALAXY_CONF_DIR=${GALAXY_CONF_DIR:-/galaxy/config} \ SLURM_CONF_DIR=${SLURM_CONF_DIR:-/etc/slurm-llnl} \ HTCONDOR_CONF_DIR=${HTCONDOR_CONF_DIR:-/htcondor} \ PULSAR_CONF_DIR=${PULSAR_CONF_DIR:-/pulsar/config} \ - KIND_CONF_DIR=${KIND_CONF_DIR:-/kind} + KIND_CONF_DIR=${KIND_CONF_DIR:-/kind} \ + IRIDA_CONF_DIR=${IRIDA_CONF_DIR:-/etc/irida} echo "Locking all configurations" -locks=("$GALAXY_CONF_DIR" "$SLURM_CONF_DIR" "$HTCONDOR_CONF_DIR" "$PULSAR_CONF_DIR" "$KIND_CONF_DIR") +locks=("$GALAXY_CONF_DIR" "$SLURM_CONF_DIR" "$HTCONDOR_CONF_DIR" "$PULSAR_CONF_DIR" "$KIND_CONF_DIR" "$IRIDA_CONF_DIR") for lock in "${locks[@]}"; do echo "Locking $lock" touch "${lock}/configurator.lock" @@ -111,6 +112,25 @@ else chmod a+r "${GALAXY_KUBECONFIG:-${KIND_CONF_DIR}/.kube/config_in_docker}" fi +# IRIDA configuration +if [ "$IRIDA_OVERWRITE_CONFIG" != "true" ]; then + echo "IRIDA_OVERWRITE_CONFIG is not true. Skipping configuration of IRIDA" +else + irida_configs=( "irida.conf" "web.conf" "static" "templates" "plugins" ) + + for conf in "${irida_configs[@]}"; do + echo "Configuring $conf" + if [[ "$conf" == *.conf ]] ; then + j2 --customize /customize.py --undefined -o "/tmp/$conf" "/templates/irida/$conf.j2" /base_config.yml + echo "The following changes will be applied to $conf:" + diff "${IRIDA_CONF_DIR}/$conf" "/tmp/$conf" + mv -f "/tmp/$conf" "${IRIDA_CONF_DIR}/$conf" + else + rsync -aP --delete "/templates/irida/$conf" "${IRIDA_CONF_DIR}/" + fi + done +fi + echo "Releasing all locks (except Galaxy) if it didn't happen already" locks=("$SLURM_CONF_DIR" "$HTCONDOR_CONF_DIR" "$PULSAR_CONF_DIR" "$KIND_CONF_DIR") for lock in "${locks[@]}"; do @@ -138,7 +158,7 @@ if [ ! -f /base_config.yml ]; then touch /base_config.yml fi -galaxy_configs=( "job_conf.xml" "galaxy.yml" "job_metrics.xml" "container_resolvers_conf.xml" "GALAXY_PROXY_PREFIX.txt" ) +galaxy_configs=( "tool_sheds_conf.xml" "job_conf.xml" "galaxy.yml" "job_metrics.xml" "container_resolvers_conf.xml" "GALAXY_PROXY_PREFIX.txt" ) for conf in "${galaxy_configs[@]}"; do echo "Configuring $conf" diff --git a/compose/galaxy-configurator/templates/galaxy/job_conf.xml.j2 b/compose/galaxy-configurator/templates/galaxy/job_conf.xml.j2 index 9b1ca49ed..1a393391d 100644 --- a/compose/galaxy-configurator/templates/galaxy/job_conf.xml.j2 +++ b/compose/galaxy-configurator/templates/galaxy/job_conf.xml.j2 @@ -36,7 +36,7 @@ /home/galaxy true {% if GALAXY_JOB_RUNNER == 'local' -%} - {{ EXPORT_DIR | regex_replace("^.", "") }}/$galaxy_root:$galaxy_root:ro,{{ EXPORT_DIR | regex_replace("^.", "") }}/$tool_directory:$tool_directory:ro,{{ EXPORT_DIR | regex_replace("^.", "") }}/$job_directory:$job_directory:rw,{{ EXPORT_DIR | regex_replace("^.", "") }}/$working_directory:$working_directory:rw,{{ EXPORT_DIR | regex_replace("^.", "") }}/$default_file_path:$default_file_path:rw + {{ EXPORT_DIR | regex_replace("^.", "") }}/$galaxy_root:$galaxy_root:ro,{{ EXPORT_DIR | regex_replace("^.", "") }}/$tool_directory:$tool_directory:ro,{{ EXPORT_DIR | regex_replace("^.", "") }}/$job_directory:$job_directory:rw,{{ EXPORT_DIR | regex_replace("^.", "") }}/$working_directory:$working_directory:rw{%if GALAXY_SINGULARITY_VOLUMES is defined-%},{{GALAXY_SINGULARITY_VOLUMES}}{%endif-%},{{ EXPORT_DIR | regex_replace("^.", "") }}/$default_file_path:$default_file_path:rw {% endif -%} {% elif GALAXY_DEPENDENCY_RESOLUTION == 'docker' -%} true diff --git a/compose/galaxy-configurator/templates/galaxy/tool_sheds_conf.xml.j2 b/compose/galaxy-configurator/templates/galaxy/tool_sheds_conf.xml.j2 new file mode 100644 index 000000000..a0173314d --- /dev/null +++ b/compose/galaxy-configurator/templates/galaxy/tool_sheds_conf.xml.j2 @@ -0,0 +1,7 @@ + + + + {% if GALAXY_ENABLE_TESTTOOLSHED %} + + {% endif %} + diff --git a/compose/galaxy-configurator/templates/irida/irida.conf.j2 b/compose/galaxy-configurator/templates/irida/irida.conf.j2 new file mode 100644 index 000000000..c38cab2f5 --- /dev/null +++ b/compose/galaxy-configurator/templates/irida/irida.conf.j2 @@ -0,0 +1,145 @@ +##### The filesystem location where files managed by irida are stored. The platform +##### will *NOT* automatically make this directory, so it must exist before you +##### start any instance of the platform. + +sequence.file.base.directory=/data/irida/sequence +reference.file.base.directory=/data/irida/reference +output.file.base.directory=/data/irida/output +assembly.file.base.directory=/data/irida/assembly + +# production / master directory store + +#sequence.file.base.directory=/cip0/software/galaxy/cbtgalaxydev/cbtgx/irida/data/irida/sequence +#reference.file.base.directory=/cip0/software/galaxy/cbtgalaxydev/cbtgx/irida/data/irida/reference +#output.file.base.directory=/cip0/software/galaxy/cbtgalaxydev/cbtgx/irida/data/irida/output + +##### Set the max upload size (in bytes). If left unconfigured, the max upload +##### size is unlimited (or limited by the container hosting IRIDA). +# file.upload.max_size= + +##### Set number of threads for FASTQC and file post-processsing. The max size +##### should not be more than the number of jdbc threads. +file.processing.core.size=4 +file.processing.max.size=8 +file.processing.queue.capacity=512 + + +# don't decompress compressed data +file.processing.decompress=false + +##### The database-specific settings. Several examples of how to specify a +##### Hibernate driver are listed below (but commented out). + +## MySQL (or MariaDB) +jdbc.driver=com.mysql.jdbc.Driver +hibernate.dialect=org.hibernate.dialect.MySQL55Dialect + +## Database location (you may need to use a different string for different +## database vendors). +jdbc.url=jdbc:mysql://irida-mysql:3306/irida_db?allowPublicKeyRetrieval=true&useSSL=false + +## Connection settings: +jdbc.username=irida_user +jdbc.password=irida_passwd + +## Configuring Liquibase to execute a schema update. Should only make changes to +## the database when executing the first time, or when upgrading. +liquibase.update.database.schema=true + +## Configure Hibernate to execute a schema construction. WARNING: do not use this +## at the same time as the Liquibase schema update. Liquibase will *not* execute +## if this value is set, warnings will be produced in the log. These settings should +## only be used in a development environment (**not** production). +hibernate.hbm2ddl.auto= +hibernate.hbm2ddl.import_files= + +## Configure Hibernate to show SQL in the log file. You *probably* don't want +## to enable this, but could be useful for debugging. +hibernate.show_sql=false + +## Connection Pool settings: +jdbc.pool.initialSize=10 +jdbc.pool.maxActive=20 +jdbc.pool.testOnBorrow=true +jdbc.pool.testOnReturn=true +jdbc.pool.testWhileIdle=true + +## Configure the JDBC library to use this query to verify that a managed +## connection is still valid. This may need to change, depending on your database vendor. +jdbc.pool.validationQuery=select 1 + +jdbc.pool.maxWait=10000 +jdbc.pool.removeAbandoned=true +jdbc.pool.logAbandoned=true +jdbc.pool.removeAbandonedTimeout=60 +jdbc.pool.maxIdle=10 + +############################################################################### +# Execution Manager configuration Galaxy. This is how IRIDA should connect to # +# the internally managed instance of Galaxy for executing workflows. # +############################################################################### + +# The URL for the Galaxy execution manager +# Networked service-to-service communication use the CONTAINER_PORT +galaxy.execution.url=http://nginx:90/ + +# The API key of an account to run workflows in Galaxy. +# This does not have to be an administrator account. +galaxy.execution.apiKey=fakekey + +# The email address of an account to run workflows in Galaxy +galaxy.execution.email=admin@galaxy.org + +# The data storage method for uploading data into a Galaxy execution manager. +galaxy.execution.dataStorage=local + +################################## +# Workflow configuration options # +################################## + +# The timeout (in seconds) for uploading files to Galaxy for execution +# Increase this value if uploading files to Galaxy is timing out. +galaxy.library.upload.timeout=10800 + +# The polling time (in seconds) for checking if files have been uploaded to Galaxy +# This value should not be greater than $galaxy.library.upload.timeout +#galaxy.library.upload.polling.time=5 + +# Number of threads used to wait for completion of uploading files. +#galaxy.library.upload.threads=1 + +# Maximum number of workflows IRIDA will schedule to run at the same time +irida.workflow.max-running=4 + +################################## +# Analysis configuration options # +################################## + +# The number days before intermediate files for an analysis get cleaned up. +# That is, the number of days before files in Galaxy get deleted for the analysis. +# Leave commented out for no cleanup. +# This value can be fractional representing a fraction of a day (e.g. 0.5 for half a day). +#irida.analysis.cleanup.days= + +################################# +# Scheduled Task configuration # +################################# +#Cron string for how often the email 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zSyteY!GS>xAC|$iyot;hGlh(VRMaYei0M%1au~V(FVolj`ETBUeA(omZLineKKXh% zPe~V7*I?1OyQte%;s2h#Y#99^uKJ3X<$L|YP91%>Niko4R!*Xw({l0)t43PGEFK9)($B z$xX>3DkQ=iT<>f8n!ctlgT6Ydu`jaSeR-kx1-b1mKUf=vzFG4ZPJR2E_zAM12#}#1 zlfJl}RJYTY#b%+psg|?e(1k#(jIxErX?8I!dV76JYI~0dOr`rj#j7p_Oqt>F+Xffyw1O*r| zXbqlIhLLoB!4}KU(+ShKu&+Y|Mn)?b7~seI|jF%485(gJb(bXn948pJL(H^_J5te zibD8nx-k0x9ZmK%T|Vj$%G(#}%5#Tql~mtO%05^8pB$10dfyvwuV?yyzYXMT`kKC` zuO|I>+pNAw75z}uQ2jx3`)coCW&3*Pg+PD*i~K;ormyL%NncGH;1}E1OASi+RpMc9 zpNGp6)9y<2@j~n#7h+4fQ2U5DSb?66y;4m0D$`)?{HpcitJa?XtK|Q&4V~#jo%iAl?R~}9y4bq@A6v3w8X-7kxBvhEC3Hnt zbYx+4WjbSWWnpw>05UK#FfB1KEiyP%F*rIgI65^kD=;!TFfgAVGDrXb03~!qSaf7z zbY(hiZ)9m^c>ppnGB7PLH!UzYR4_FxQ%d0000 + + + COMBAT-SARS-COV-2 Explorer + + + + + + + +

+
+
+
+ +
+
+
+

COMBAT SARS-COV-2 Workbench

+

The COMBAT-SARS-COV-2 Workbench provides easy to use tools for analysing SARS-COV-2 genomic + sequence samples.

+

It was developed at part of the COMBAT-SARS-COV-2 project, an Africa CDC funded + project undertaken by researchers and software developers at SANBI. The COMBAT-SARS-COV-2 + Workbench is developed using technology from the IRIDA and + Galaxy projects and incorporates leading tools developed for SARS-COV-2 + and microbial bioinformatics.

+
+
+
+
+
+
+ SANBI logo +
+
+ UWC logo +
+
+
+
+ SA MRC logo +
+
+ SA Department of Science and Innovation logo +
+
+ NRF logo +
+
+
+ + + + diff --git a/compose/galaxy-configurator/templates/irida/web.conf.j2 b/compose/galaxy-configurator/templates/irida/web.conf.j2 new file mode 100644 index 000000000..453782807 --- /dev/null +++ b/compose/galaxy-configurator/templates/irida/web.conf.j2 @@ -0,0 +1,24 @@ +# The externally visible URL for accessing this instance of IRIDA. This key is +# used by the e-mailer when sending out e-mail notifications (password resets, +# for example) and embeds this URL directly in the body of the e-mail. +server.base.url=http://0.0.0.0:8080 + +# Mail server configuration settings +mail.server.host=your-mail-server.local +mail.server.protocol=smtp +mail.server.email=admin@sanbi.ac.za +mail.server.username=IRIDA Platform + +# Location of the IRIDA Platform updates file +# updates.file=/etc/irida/updates.md + +# The title and link for an external help resource. Uncomment these +# and modify to have your own link rendered in the 'Help' menu. If these +# are left commented out, no link appears under the 'Help' menu. +# help.page.title=Your Help Page Title +# help.page.url=http://www.example.org/help + +# The e-mail address for contacting an administrator for help. Uncomment +# this and modify to have your own e-mail address rendered in the 'Help' menu. +# If this is left commented out, no contact e-mail appears in the 'Help' menu. +# help.contact.email=you@example.org diff --git a/compose/galaxy-configurator/templates/nginx/nginx.conf.j2 b/compose/galaxy-configurator/templates/nginx/nginx.conf.j2 index fc348c448..4463d9147 100644 --- a/compose/galaxy-configurator/templates/nginx/nginx.conf.j2 +++ b/compose/galaxy-configurator/templates/nginx/nginx.conf.j2 @@ -19,15 +19,36 @@ http { # maximum file upload size client_max_body_size 10g; + {% if IRIDA_ENABLED | default %} server { + # this is for IRIDA listen 80 default_server; listen [::]:80 default_server; server_name _; + proxy_read_timeout 600; + proxy_connect_timeout 600; + proxy_send_timeout 600; + + location / { + proxy_set_header X-Forwarded-Host $host; + proxy_set_header X-Forwarded-Server $host; + proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for; + proxy_pass http://irida-web:8080; + } + } + {% endif %} + + server { + listen {%if IRIDA_ENABLED %} 90 {% else %} 80 {% endif %} default_server; + listen [::]:{%if IRIDA_ENABLED %}90{% else %}80{% endif %} default_server; + server_name _; + # use a variable for convenience set $galaxy_static /export/galaxy/static; set $galaxy_root /export/galaxy; + # proxy all requests not matching other locations to uWSGI location /{{ GALAXY_PROXY_PREFIX | regex_replace("^/", "") | regex_replace("/$", "") }} { uwsgi_pass galaxy-server:5555; diff --git a/compose/galaxy-server/Dockerfile b/compose/galaxy-server/Dockerfile index d789c2250..1739fca21 100644 --- a/compose/galaxy-server/Dockerfile +++ b/compose/galaxy-server/Dockerfile @@ -50,7 +50,7 @@ RUN curl -s -L "https://repo.anaconda.com/miniconda/Miniconda3-${MINICONDA_VERSI FROM build_base as build_galaxy -ARG GALAXY_RELEASE=release_20.09 +ARG GALAXY_RELEASE=release_21.01 ARG GALAXY_REPO=https://github.com/galaxyproject/galaxy COPY ./files/common_cleanup.sh /usr/bin/common_cleanup.sh @@ -83,7 +83,7 @@ ENV EXPORT_DIR=/export \ GALAXY_PYTHON=/usr/bin/python3 \ HTCONDOR_ROOT=/opt/htcondor -ENV GALAXY_RELEASE=${GALAXY_RELEASE:-release_20.09} \ +ENV GALAXY_RELEASE=${GALAXY_RELEASE:-release_21.01} \ GALAXY_REPO=${GALAXY_REPO:-https://github.com/galaxyproject/galaxy} \ GALAXY_STATIC_DIR=$GALAXY_ROOT/static \ GALAXY_EXPORT=$EXPORT_DIR/galaxy \ @@ -130,6 +130,10 @@ COPY --chown=$GALAXY_USER:$GALAXY_USER --from=build_miniconda /etc/profile.d/con COPY ./files/start.sh /usr/bin/start.sh +RUN usermod -aG root $GALAXY_USER + +#RUN if [ -n "$GALAXY_EXTRA_GROUP" ] ; then usermod -a -G $GALAXY_EXTRA_GROUP $GALAXY_USER ; fi + EXPOSE 80 ENTRYPOINT "/usr/bin/start.sh" diff --git a/compose/galaxy-server/files/start.sh b/compose/galaxy-server/files/start.sh index 860280856..380a6b335 100755 --- a/compose/galaxy-server/files/start.sh +++ b/compose/galaxy-server/files/start.sh @@ -3,7 +3,7 @@ create_user() { GALAXY_PROXY_PREFIX=$(cat $GALAXY_CONFIG_DIR/GALAXY_PROXY_PREFIX.txt) echo "Waiting for Galaxy..." - until [ "$(curl -s -o /dev/null -w '%{http_code}' ${GALAXY_URL:-nginx}$GALAXY_PROXY_PREFIX)" -eq "200" ] && echo Galaxy started; do + until [ "$(curl -L -s -o /dev/null -w '%{http_code}' ${GALAXY_URL:-nginx}$GALAXY_PROXY_PREFIX)" -eq "200" ] && echo Galaxy started; do sleep 0.1; done; echo "Creating admin user $GALAXY_DEFAULT_ADMIN_USER with key $GALAXY_DEFAULT_ADMIN_KEY and password $GALAXY_DEFAULT_ADMIN_PASSWORD if not existing" @@ -80,9 +80,9 @@ fi if $PRIVILEGED; then echo "Mounting CVMFS" chmod 666 /dev/fuse - mkdir /cvmfs/data.galaxyproject.org + if [ ! -d /cvmfs/data.galaxyproject.org ] ; then mkdir /cvmfs/data.galaxyproject.org ; fi mount -t cvmfs data.galaxyproject.org /cvmfs/data.galaxyproject.org - mkdir /cvmfs/singularity.galaxyproject.org + if [ ! -d /cvmfs/singularity.galaxyproject.org ] ; then mkdir /cvmfs/singularity.galaxyproject.org ; fi mount -t cvmfs singularity.galaxyproject.org /cvmfs/singularity.galaxyproject.org fi diff --git a/compose/irida/Dockerfile b/compose/irida/Dockerfile new file mode 100644 index 000000000..f42e80bfc --- /dev/null +++ b/compose/irida/Dockerfile @@ -0,0 +1,67 @@ +FROM tomcat:9.0 +LABEL Maintainer="combat-sars-cov-2-help@sanbi.ac.za" + +ARG USER=galaxy +ARG UID=1450 +ARG GID=1450 +# default password for user +ARG PW=galaxy + +RUN apt-get update; \ + apt-get -y upgrade; \ + apt-get install -f ; \ + apt-get install -y perl fastqc wget gpg; \ + rm -rf /var/lib/apt/lists/*; \ + mkdir -p /etc/irida/plugins + +RUN useradd -m ${USER} --uid=${UID} && echo "${USER}:${PW}" | \ + chpasswd + +ENV GOSU_VERSION 1.10 +RUN set -ex; \ + apt-get install -y --no-install-recommends ca-certificates; \ + rm -rf /var/lib/apt/lists/*; \ + dpkgArch="$(dpkg --print-architecture | awk -F- '{ print $NF }')"; \ + wget -O /usr/local/bin/gosu "https://github.com/tianon/gosu/releases/download/$GOSU_VERSION/gosu-$dpkgArch"; \ + wget -O /usr/local/bin/gosu.asc "https://github.com/tianon/gosu/releases/download/$GOSU_VERSION/gosu-$dpkgArch.asc"; \ + export GNUPGHOME="$(mktemp -d)"; \ + gpg --keyserver keyserver.ubuntu.com --recv-keys B42F6819007F00F88E364FD4036A9C25BF357DD4; \ + gpg --batch --verify /usr/local/bin/gosu.asc /usr/local/bin/gosu; \ + rm -r "$GNUPGHOME" /usr/local/bin/gosu.asc; \ + chmod +x /usr/local/bin/gosu; \ + gosu nobody true; + +ENV IRIDA_DOWNLOAD_URL="https://github.com/phac-nml/irida/releases/download/" \ + IRIDA_VERSION="21.09" \ + IRIDA_DATA_DIR=/data/irida \ + JAVA_OPTS="-Dspring.profiles.active=prod -Dirida.db.profile=prod" \ + GALAXY_ADMIN_USER="admin@galaxy.org" + + +RUN mkdir -p $IRIDA_DATA_DIR; \ + bash -c "mkdir -p ${IRIDA_DATA_DIR}/{sequence,reference,output,assembly}"; \ + wget "${IRIDA_DOWNLOAD_URL}/${IRIDA_VERSION}/irida-${IRIDA_VERSION}.war"; \ + mv irida-${IRIDA_VERSION}.war /usr/local/tomcat/webapps/ROOT.war + +USER ${USER} + +VOLUME $IRIDA_DATA_DIR + +USER root + +COPY *.conf /etc/irida/ +COPY *.sh ./ + +COPY etc-irida/static /etc/irida/static +COPY etc-irida/templates /etc/irida/templates + +COPY start-daemons.sh /usr/local/bin/start-daemons.sh +RUN chmod a+x /usr/local/bin/start-daemons.sh + +#install the irida plugins +RUN wget -P /etc/irida/plugins https://github.com/COMBAT-SARS-COV-2/irida-plugin-sars-cov-2-nanopore/releases/download/0.1.4/sarscov2-artic-nanopore-pipeline-plugin-0.1.4.jar +RUN wget -P /etc/irida/plugins https://github.com/COMBAT-SARS-COV-2/irida-plugin-sars-cov-2-illumina/releases/download/0.1.8/sarscov2-artic-illumina-pipeline-plugin-0.1.8.jar + +ENTRYPOINT ["./docker-entrypoint.sh"] + +CMD ["./wait-for-it.sh", "irida_mysql:33060", "--", "/usr/local/bin/start-daemons.sh"] diff --git a/compose/irida/docker-entrypoint.sh b/compose/irida/docker-entrypoint.sh new file mode 100755 index 000000000..aa01c172d --- /dev/null +++ b/compose/irida/docker-entrypoint.sh @@ -0,0 +1,26 @@ +#!/bin/bash +set -e + +if [ "$1" = './wait-for-it.sh' ]; then + if [ -z "$(getent passwd $RUN_USER)" ]; then + echo "Creating user $RUN_USER:$RUN_GROUP" + mkdir -p ${IRIDA_DATA_DIR} + groupadd --gid ${RUN_GROUP_GID} -r ${RUN_GROUP} && \ + useradd --uid ${RUN_USER_UID} -g ${RUN_GROUP} -d /home/${CATALINA_HOME} ${RUN_USER} + rm -rf ${CATALINA_HOME}/logs + rm -rf ${CATALINA_HOME}/webapps + rm -rf ${CATALINA_HOME}/temp + chown -R ${RUN_USER}:${RUN_GROUP} ${CATALINA_HOME}/ \ + && gosu ${RUN_USER} mkdir -p ${CATALINA_HOME}/logs \ + && gosu ${RUN_USER} mkdir -p ${CATALINA_HOME}/webapps \ + && gosu ${RUN_USER} mkdir -p ${CATALINA_HOME}/temp \ + && chown -R ${RUN_USER}:${RUN_GROUP} ${CATALINA_HOME}/work \ + && chown -R ${RUN_USER}:${RUN_GROUP} ${CATALINA_HOME}/conf \ + && chown -R ${RUN_USER}:${RUN_GROUP} ${IRIDA_DATA_DIR} . \ + && gosu ${RUN_USER} mkdir -p ${IRIDA_DATA_DIR}/{sequence,reference,output,assembly} + fi + + exec gosu "${RUN_USER}:${RUN_GROUP}" "$@" +fi + +exec "$@" diff --git a/compose/irida/etc-irida/static/css/bootstrap.min.css 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zSyteY!GS>xAC|$iyot;hGlh(VRMaYei0M%1au~V(FVolj`ETBUeA(omZLineKKXh% zPe~V7*I?1OyQte%;s2h#Y#99^uKJ3X<$L|YP91%>Niko4R!*Xw({l0)t43PGEFK9)($B z$xX>3DkQ=iT<>f8n!ctlgT6Ydu`jaSeR-kx1-b1mKUf=vzFG4ZPJR2E_zAM12#}#1 zlfJl}RJYTY#b%+psg|?e(1k#(jIxErX?8I!dV76JYI~0dOr`rj#j7p_Oqt>F+Xffyw1O*r| zXbqlIhLLoB!4}KU(+ShKu&+Y|Mn)?b7~seI|jF%485(gJb(bXn948pJL(H^_J5te zibD8nx-k0x9ZmK%T|Vj$%G(#}%5#Tql~mtO%05^8pB$10dfyvwuV?yyzYXMT`kKC` zuO|I>+pNAw75z}uQ2jx3`)coCW&3*Pg+PD*i~K;ormyL%NncGH;1}E1OASi+RpMc9 zpNGp6)9y<2@j~n#7h+4fQ2U5DSb?66y;4m0D$`)?{HpcitJa?XtK|Q&4V~#jo%iAl?R~}9y4bq@A6v3w8X-7kxBvhEC3Hnt zbYx+4WjbSWWnpw>05UK#FfB1KEiyP%F*rIgI65^kD=;!TFfgAVGDrXb03~!qSaf7z zbY(hiZ)9m^c>ppnGB7PLH!UzYR4_FxQ%d0000 + + + COMBAT-SARS-COV-2 Explorer + + + + + + + +
+
+
+
+ +
+
+
+

COMBAT SARS-COV-2 Workbench

+

The COMBAT-SARS-COV-2 Workbench provides easy to use tools for analysing SARS-COV-2 genomic + sequence samples.

+

It was developed at part of the COMBAT-SARS-COV-2 project, an Africa CDC funded + project undertaken by researchers and software developers at SANBI. The COMBAT-SARS-COV-2 + Workbench is developed using technology from the IRIDA and + Galaxy projects and incorporates leading tools developed for SARS-COV-2 + and microbial bioinformatics.

+
+
+
+
+
+
+ SANBI logo +
+
+ UWC logo +
+
+
+
+ SA MRC logo +
+
+ SA Department of Science and Innovation logo +
+
+ NRF logo +
+
+
+ + + + diff --git a/compose/irida/galaxy_tools.yml b/compose/irida/galaxy_tools.yml new file mode 100644 index 000000000..0d32229e0 --- /dev/null +++ b/compose/irida/galaxy_tools.yml @@ -0,0 +1,82 @@ +install_repository_dependencies: true +install_resolver_dependencies: true +install_tool_dependencies: true +tools: +- name: ivar_variants + owner: iuc + revisions: + - 3888bbe7a9ca + tool_panel_section_label: Tools from workflows + tool_shed_url: https://toolshed.g2.bx.psu.edu/ +- name: multiqc + owner: iuc + revisions: + - 75c93c70d094 + tool_panel_section_label: Tools from workflows + tool_shed_url: https://toolshed.g2.bx.psu.edu/ +- name: bwa + owner: devteam + revisions: + - 64f11cf59c6e + tool_panel_section_label: Tools from workflows + tool_shed_url: https://toolshed.g2.bx.psu.edu/ +- name: qualimap_bamqc + owner: iuc + revisions: + - e7fd6754d093 + tool_panel_section_label: Tools from workflows + tool_shed_url: https://toolshed.g2.bx.psu.edu/ +- name: pangolin + owner: iuc + revisions: + - debfccc4d65b + tool_panel_section_label: Tools from workflows + tool_shed_url: https://toolshed.g2.bx.psu.edu/ +- name: nextclade + owner: iuc + revisions: + - b74b9a7b3e3b + tool_panel_section_label: Tools from workflows + tool_shed_url: https://toolshed.g2.bx.psu.edu/ +- name: ivar_trim + owner: iuc + revisions: + - c092052ed673 + tool_panel_section_label: Tools from workflows + tool_shed_url: https://toolshed.g2.bx.psu.edu/ +- name: picard + owner: devteam + revisions: + - 7d34178f2812 + tool_panel_section_label: Tools from workflows + tool_shed_url: https://toolshed.g2.bx.psu.edu/ +- name: qc + owner: sanbi-uwc + revisions: + - 6bdec8c62aec + tool_panel_section_label: Tools from workflows + tool_shed_url: https://testtoolshed.g2.bx.psu.edu/ +- name: text_processing + owner: bgruening + revisions: + - 9ff72e942410 + tool_panel_section_label: Tools from workflows + tool_shed_url: https://toolshed.g2.bx.psu.edu/ +- name: samtools_view + owner: iuc + revisions: + - b72793637686 + tool_panel_section_label: Tools from workflows + tool_shed_url: https://toolshed.g2.bx.psu.edu/ +- name: fastp + owner: iuc + revisions: + - dbf9c561ef29 + tool_panel_section_label: Tools from workflows + tool_shed_url: https://toolshed.g2.bx.psu.edu/ +- name: ivar_consensus + owner: iuc + revisions: + - 731182d54f78 + tool_panel_section_label: Tools from workflows + tool_shed_url: https://toolshed.g2.bx.psu.edu/ diff --git a/compose/irida/irida.conf b/compose/irida/irida.conf new file mode 100644 index 000000000..09b48d994 --- /dev/null +++ b/compose/irida/irida.conf @@ -0,0 +1,142 @@ +##### The filesystem location where files managed by irida are stored. The platform +##### will *NOT* automatically make this directory, so it must exist before you +##### start any instance of the platform. + +sequence.file.base.directory=/data/irida/sequence +reference.file.base.directory=/data/irida/reference +output.file.base.directory=/data/irida/output +assembly.file.base.directory=/data/irida/assembly + +# production / master directory store + +#sequence.file.base.directory=/cip0/software/galaxy/cbtgalaxydev/cbtgx/irida/data/irida/sequence +#reference.file.base.directory=/cip0/software/galaxy/cbtgalaxydev/cbtgx/irida/data/irida/reference +#output.file.base.directory=/cip0/software/galaxy/cbtgalaxydev/cbtgx/irida/data/irida/output + +##### Set the max upload size (in bytes). If left unconfigured, the max upload +##### size is unlimited (or limited by the container hosting IRIDA). +# file.upload.max_size= + +##### Set number of threads for FASTQC and file post-processsing. The max size +##### should not be more than the number of jdbc threads. +file.processing.core.size=4 +file.processing.max.size=8 +file.processing.queue.capacity=512 + + +##### The database-specific settings. Several examples of how to specify a +##### Hibernate driver are listed below (but commented out). + +## MySQL (or MariaDB) +jdbc.driver=com.mysql.jdbc.Driver +hibernate.dialect=org.hibernate.dialect.MySQL55Dialect + +## Database location (you may need to use a different string for different +## database vendors). +jdbc.url=jdbc:mysql://irida-mysql:3306/irida_db?allowPublicKeyRetrieval=true&useSSL=false + +## Connection settings: +jdbc.username=irida_user +jdbc.password=irida_passwd + +## Configuring Liquibase to execute a schema update. Should only make changes to +## the database when executing the first time, or when upgrading. +liquibase.update.database.schema=true + +## Configure Hibernate to execute a schema construction. WARNING: do not use this +## at the same time as the Liquibase schema update. Liquibase will *not* execute +## if this value is set, warnings will be produced in the log. These settings should +## only be used in a development environment (**not** production). +hibernate.hbm2ddl.auto= +hibernate.hbm2ddl.import_files= + +## Configure Hibernate to show SQL in the log file. You *probably* don't want +## to enable this, but could be useful for debugging. +hibernate.show_sql=false + +## Connection Pool settings: +jdbc.pool.initialSize=10 +jdbc.pool.maxActive=20 +jdbc.pool.testOnBorrow=true +jdbc.pool.testOnReturn=true +jdbc.pool.testWhileIdle=true + +## Configure the JDBC library to use this query to verify that a managed +## connection is still valid. This may need to change, depending on your database vendor. +jdbc.pool.validationQuery=select 1 + +jdbc.pool.maxWait=10000 +jdbc.pool.removeAbandoned=true +jdbc.pool.logAbandoned=true +jdbc.pool.removeAbandonedTimeout=60 +jdbc.pool.maxIdle=10 + +############################################################################### +# Execution Manager configuration Galaxy. This is how IRIDA should connect to # +# the internally managed instance of Galaxy for executing workflows. # +############################################################################### + +# The URL for the Galaxy execution manager +# Networked service-to-service communication use the CONTAINER_PORT +galaxy.execution.url=http://nginx/galaxy + +# The API key of an account to run workflows in Galaxy. +# This does not have to be an administrator account. +galaxy.execution.apiKey=fakekey + +# The email address of an account to run workflows in Galaxy +galaxy.execution.email=admin@galaxy.org + +# The data storage method for uploading data into a Galaxy execution manager. +galaxy.execution.dataStorage=local + +################################## +# Workflow configuration options # +################################## + +# The timeout (in seconds) for uploading files to Galaxy for execution +# Increase this value if uploading files to Galaxy is timing out. +galaxy.library.upload.timeout=10800 + +# The polling time (in seconds) for checking if files have been uploaded to Galaxy +# This value should not be greater than $galaxy.library.upload.timeout +#galaxy.library.upload.polling.time=5 + +# Number of threads used to wait for completion of uploading files. +#galaxy.library.upload.threads=1 + +# Maximum number of workflows IRIDA will schedule to run at the same time +irida.workflow.max-running=4 + +################################## +# Analysis configuration options # +################################## + +# The number days before intermediate files for an analysis get cleaned up. +# That is, the number of days before files in Galaxy get deleted for the analysis. +# Leave commented out for no cleanup. +# This value can be fractional representing a fraction of a day (e.g. 0.5 for half a day). +#irida.analysis.cleanup.days= + +################################# +# Scheduled Task configuration # +################################# +#Cron string for how often the email subscriptions are sent out. +#Format: sec min hrs dom mon dow +irida.scheduled.subscription.cron=0 0 0 * * * +irida.scheduled.threads=2 + +################################# +# NCBI SRA Export configuration # +################################# +#Host to upload ncbi exports +ncbi.upload.host=localhost +#FTP Username and password for bulk SRA uploads +ncbi.upload.user=test +ncbi.upload.password=password +#base directory in which to create SRA submissions +ncbi.upload.baseDirectory=tmp +#port for ftp upload +ncbi.upload.port=21 +#Default namespace to preface file identifiers +ncbi.upload.namespace=IRIDA diff --git a/compose/irida/nginx-config b/compose/irida/nginx-config new file mode 100644 index 000000000..48b6bd889 --- /dev/null +++ b/compose/irida/nginx-config @@ -0,0 +1,19 @@ +server { + listen 80; + + client_max_body_size 50g; + + proxy_read_timeout 600; + proxy_connect_timeout 600; + proxy_send_timeout 600; + + access_log /var/log/nginx/tomcat-access.log; + error_log /var/log/nginx/tomcat-error.log; + + location / { + proxy_set_header X-Forwarded-Host $host; + proxy_set_header X-Forwarded-Server $host; + proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for; + proxy_pass http://127.0.0.1:8080; + } +} diff --git a/compose/irida/start-daemons.sh b/compose/irida/start-daemons.sh new file mode 100644 index 000000000..dcd67fdc6 --- /dev/null +++ b/compose/irida/start-daemons.sh @@ -0,0 +1,3 @@ +#!/bin/sh + +/usr/local/tomcat/bin/catalina.sh run diff --git a/compose/irida/tmp/META-INF/MANIFEST.MF b/compose/irida/tmp/META-INF/MANIFEST.MF new file mode 100644 index 000000000..1b3eb2f25 --- /dev/null +++ b/compose/irida/tmp/META-INF/MANIFEST.MF @@ -0,0 +1,12 @@ +Manifest-Version: 1.0 +Created-By: Apache Maven 3.6.3 +Built-By: root +Build-Jdk: 11.0.9 +Plugin-Class: ca.corefacility.bioinformatics.irida.plugins.ArticIllumina + Plugin +Plugin-Dependencies: +Plugin-Id: sarscov2-artic-illumina-pipeline-plugin +Plugin-Provider: COMBAT-SARS-COV-2 (SANBI) +Plugin-Requires: 1.1.0 +Plugin-Version: 0.1.9 + diff --git a/compose/irida/tmp/META-INF/extensions.idx b/compose/irida/tmp/META-INF/extensions.idx new file mode 100644 index 000000000..68b758c7d --- /dev/null +++ b/compose/irida/tmp/META-INF/extensions.idx @@ -0,0 +1,2 @@ +# Generated by PF4J +ca.corefacility.bioinformatics.irida.plugins.ArticIlluminaPlugin$PluginInfo diff --git a/compose/irida/tmp/META-INF/maven/ca.corefacility.bioinformatics.irida.plugins/sarscov2-artic-illumina-pipeline-plugin/pom.properties b/compose/irida/tmp/META-INF/maven/ca.corefacility.bioinformatics.irida.plugins/sarscov2-artic-illumina-pipeline-plugin/pom.properties new file mode 100644 index 000000000..4eba3f600 --- /dev/null +++ b/compose/irida/tmp/META-INF/maven/ca.corefacility.bioinformatics.irida.plugins/sarscov2-artic-illumina-pipeline-plugin/pom.properties @@ -0,0 +1,4 @@ +#Created by Apache Maven 3.6.3 +groupId=ca.corefacility.bioinformatics.irida.plugins +artifactId=sarscov2-artic-illumina-pipeline-plugin +version=0.1.9 diff --git a/compose/irida/tmp/META-INF/maven/ca.corefacility.bioinformatics.irida.plugins/sarscov2-artic-illumina-pipeline-plugin/pom.xml b/compose/irida/tmp/META-INF/maven/ca.corefacility.bioinformatics.irida.plugins/sarscov2-artic-illumina-pipeline-plugin/pom.xml new file mode 100644 index 000000000..3bc5ee0a4 --- /dev/null +++ b/compose/irida/tmp/META-INF/maven/ca.corefacility.bioinformatics.irida.plugins/sarscov2-artic-illumina-pipeline-plugin/pom.xml @@ -0,0 +1,96 @@ + + + 4.0.0 + + ca.corefacility.bioinformatics.irida.plugins + sarscov2-artic-illumina-pipeline-plugin + 0.1.9 + + + + + sarscov2-artic-illumina-pipeline-plugin + ca.corefacility.bioinformatics.irida.plugins.ArticIlluminaPlugin + 0.1.9 + COMBAT-SARS-COV-2 (SANBI) + + 1.1.0 + + + 21.05 + + + 2.4.0 + + + 11 + 11 + + UTF-8 + + + + + + ca.corefacility.bioinformatics + irida + ${irida.version.compiletime} + classes + provided + + + + org.pf4j + pf4j + 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Tool: multiqc - Workflow Step #: 3 +#Wed Mar 10 15:55:24 SAST 2021 +pipeline.parameters.articillumina.multiqc-3-comment=Custom comment +pipeline.parameters.articillumina.multiqc-3-title=Report title +#Tool Parameters - Tool: bwa - Workflow Step #: 4 +#Wed Mar 10 15:55:24 SAST 2021 +pipeline.parameters.articillumina.bwa-4-fastq_input.fastq_input_selector=Single or Paired-end reads +pipeline.parameters.articillumina.bwa-4-reference_source.reference_source_selector=bwa-4-reference_source.reference_source_selector +pipeline.parameters.articillumina.bwa-4-reference_source.index_a=bwa-4-reference_source.index_a +pipeline.parameters.articillumina.bwa-4-analysis_type.analysis_type_selector=Select analysis mode +pipeline.parameters.articillumina.bwa-4-fastq_input.iset_stats=Enter mean, standard deviation, max, and min for insert lengths. +pipeline.parameters.articillumina.bwa-4-rg.rg_selector=bwa-4-rg.rg_selector +#Tool Parameters - Tool: picard - Workflow Step #: 5 +#Wed Mar 10 15:55:24 SAST 2021 +pipeline.parameters.articillumina.picard-5-barcode_tag=picard-5-barcode_tag +pipeline.parameters.articillumina.picard-5-read_name_regex=picard-5-read_name_regex +pipeline.parameters.articillumina.picard-5-duplicate_scoring_strategy=picard-5-duplicate_scoring_strategy +pipeline.parameters.articillumina.picard-5-validation_stringency=picard-5-validation_stringency +#Tool Parameters - 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Tool: multiqc - Workflow Step #: 3 +#Wed Apr 07 10:26:30 SAST 2021 +pipeline.parameters.artic_illumina.multiqc-3-title=Report title +pipeline.parameters.artic_illumina.multiqc-3-comment=Custom comment +#Tool Parameters - Tool: bwa - Workflow Step #: 4 +#Wed Apr 07 10:26:30 SAST 2021 +pipeline.parameters.artic_illumina.bwa-4-reference_source.index_a=bwa-4-reference_source.index_a +pipeline.parameters.artic_illumina.bwa-4-fastq_input.iset_stats=Enter mean, standard deviation, max, and min for insert lengths. +pipeline.parameters.artic_illumina.bwa-4-analysis_type.analysis_type_selector=Select analysis mode +pipeline.parameters.artic_illumina.bwa-4-fastq_input.fastq_input_selector=Single or Paired-end reads +pipeline.parameters.artic_illumina.bwa-4-rg.rg_selector=bwa-4-rg.rg_selector +pipeline.parameters.artic_illumina.bwa-4-reference_source.reference_source_selector=bwa-4-reference_source.reference_source_selector +#Tool Parameters - Tool: picard - Workflow Step #: 5 +#Wed Apr 07 10:26:30 SAST 2021 +pipeline.parameters.artic_illumina.picard-5-duplicate_scoring_strategy=picard-5-duplicate_scoring_strategy +pipeline.parameters.artic_illumina.picard-5-validation_stringency=picard-5-validation_stringency +pipeline.parameters.artic_illumina.picard-5-barcode_tag=picard-5-barcode_tag +pipeline.parameters.artic_illumina.picard-5-read_name_regex=picard-5-read_name_regex +#Tool Parameters - Tool: samtool_filter2 - Workflow Step #: 6 +#Wed Apr 07 10:26:30 SAST 2021 +pipeline.parameters.artic_illumina.samtool_filter2-6-outputtype=Select the output format +pipeline.parameters.artic_illumina.samtool_filter2-6-regions=Select regions (only used when the input is in BAM format) +pipeline.parameters.artic_illumina.samtool_filter2-6-library=Select alignments from Library +pipeline.parameters.artic_illumina.samtool_filter2-6-header=Header in output +pipeline.parameters.artic_illumina.samtool_filter2-6-flag.filter=Filter on bitwise flag +pipeline.parameters.artic_illumina.samtool_filter2-6-read_group=Select alignments from Read Group +#Tool Parameters - Tool: ivar_trim - Workflow Step #: 7 +#Wed Apr 07 10:26:30 SAST 2021 +pipeline.parameters.artic_illumina.ivar_trim-7-primer.cached_bed=Primer scheme name +pipeline.parameters.artic_illumina.ivar_trim-7-primer.source=Source of primer information +#Tool Parameters - Tool: qualimap_bamqc - Workflow Step #: 8 +#Wed Apr 07 10:26:30 SAST 2021 +pipeline.parameters.artic_illumina.qualimap_bamqc-8-plot_specific.homopolymer_size=Homopolymer size +pipeline.parameters.artic_illumina.qualimap_bamqc-8-plot_specific.n_bins=Number of bins to use in across-reference plots +pipeline.parameters.artic_illumina.qualimap_bamqc-8-plot_specific.paint_chromosome_limits=Draw chromosome limits +pipeline.parameters.artic_illumina.qualimap_bamqc-8-stats_regions.region_select=Reference genome regions to calculate mapping statistics for +#Tool Parameters - 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Tool: multiqc - Workflow Step #: 3 +#Wed Apr 07 10:26:30 SAST 2021 +pipeline.parameters.artic_illumina.multiqc-3-title=Report title +pipeline.parameters.artic_illumina.multiqc-3-comment=Custom comment +#Tool Parameters - Tool: bwa - Workflow Step #: 4 +#Wed Apr 07 10:26:30 SAST 2021 +pipeline.parameters.artic_illumina.bwa-4-reference_source.index_a=bwa-4-reference_source.index_a +pipeline.parameters.artic_illumina.bwa-4-fastq_input.iset_stats=Enter mean, standard deviation, max, and min for insert lengths. +pipeline.parameters.artic_illumina.bwa-4-analysis_type.analysis_type_selector=Select analysis mode +pipeline.parameters.artic_illumina.bwa-4-fastq_input.fastq_input_selector=Single or Paired-end reads +pipeline.parameters.artic_illumina.bwa-4-rg.rg_selector=bwa-4-rg.rg_selector +pipeline.parameters.artic_illumina.bwa-4-reference_source.reference_source_selector=bwa-4-reference_source.reference_source_selector +#Tool Parameters - Tool: picard - Workflow Step #: 5 +#Wed Apr 07 10:26:30 SAST 2021 +pipeline.parameters.artic_illumina.picard-5-duplicate_scoring_strategy=picard-5-duplicate_scoring_strategy +pipeline.parameters.artic_illumina.picard-5-validation_stringency=picard-5-validation_stringency +pipeline.parameters.artic_illumina.picard-5-barcode_tag=picard-5-barcode_tag +pipeline.parameters.artic_illumina.picard-5-read_name_regex=picard-5-read_name_regex +#Tool Parameters - Tool: samtool_filter2 - Workflow Step #: 6 +#Wed Apr 07 10:26:30 SAST 2021 +pipeline.parameters.artic_illumina.samtool_filter2-6-outputtype=Select the output format +pipeline.parameters.artic_illumina.samtool_filter2-6-regions=Select regions (only used when the input is in BAM format) +pipeline.parameters.artic_illumina.samtool_filter2-6-library=Select alignments from Library +pipeline.parameters.artic_illumina.samtool_filter2-6-header=Header in output +pipeline.parameters.artic_illumina.samtool_filter2-6-flag.filter=Filter on bitwise flag +pipeline.parameters.artic_illumina.samtool_filter2-6-read_group=Select alignments from Read Group +#Tool Parameters - Tool: ivar_trim - Workflow Step #: 7 +#Wed Apr 07 10:26:30 SAST 2021 +pipeline.parameters.artic_illumina.ivar_trim-7-primer.cached_bed=Primer scheme name +pipeline.parameters.artic_illumina.ivar_trim-7-primer.source=Source of primer information +#Tool Parameters - Tool: qualimap_bamqc - Workflow Step #: 8 +#Wed Apr 07 10:26:30 SAST 2021 +pipeline.parameters.artic_illumina.qualimap_bamqc-8-plot_specific.homopolymer_size=Homopolymer size +pipeline.parameters.artic_illumina.qualimap_bamqc-8-plot_specific.n_bins=Number of bins to use in across-reference plots +pipeline.parameters.artic_illumina.qualimap_bamqc-8-plot_specific.paint_chromosome_limits=Draw chromosome limits +pipeline.parameters.artic_illumina.qualimap_bamqc-8-stats_regions.region_select=Reference genome regions to calculate mapping statistics for +#Tool Parameters - 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Tool: multiqc - Workflow Step #: 3 +#Wed Apr 07 10:26:30 SAST 2021 +pipeline.parameters.artic_illumina.multiqc-3-title=Report title +pipeline.parameters.artic_illumina.multiqc-3-comment=Custom comment +#Tool Parameters - Tool: bwa - Workflow Step #: 4 +#Wed Apr 07 10:26:30 SAST 2021 +pipeline.parameters.artic_illumina.bwa-4-reference_source.index_a=bwa-4-reference_source.index_a +pipeline.parameters.artic_illumina.bwa-4-fastq_input.iset_stats=Enter mean, standard deviation, max, and min for insert lengths. +pipeline.parameters.artic_illumina.bwa-4-analysis_type.analysis_type_selector=Select analysis mode +pipeline.parameters.artic_illumina.bwa-4-fastq_input.fastq_input_selector=Single or Paired-end reads +pipeline.parameters.artic_illumina.bwa-4-rg.rg_selector=bwa-4-rg.rg_selector +pipeline.parameters.artic_illumina.bwa-4-reference_source.reference_source_selector=bwa-4-reference_source.reference_source_selector +#Tool Parameters - Tool: picard - Workflow Step #: 5 +#Wed Apr 07 10:26:30 SAST 2021 +pipeline.parameters.artic_illumina.picard-5-duplicate_scoring_strategy=picard-5-duplicate_scoring_strategy +pipeline.parameters.artic_illumina.picard-5-validation_stringency=picard-5-validation_stringency +pipeline.parameters.artic_illumina.picard-5-barcode_tag=picard-5-barcode_tag +pipeline.parameters.artic_illumina.picard-5-read_name_regex=picard-5-read_name_regex +#Tool Parameters - Tool: samtool_filter2 - Workflow Step #: 6 +#Wed Apr 07 10:26:30 SAST 2021 +pipeline.parameters.artic_illumina.samtool_filter2-6-outputtype=Select the output format +pipeline.parameters.artic_illumina.samtool_filter2-6-regions=Select regions (only used when the input is in BAM format) +pipeline.parameters.artic_illumina.samtool_filter2-6-library=Select alignments from Library +pipeline.parameters.artic_illumina.samtool_filter2-6-header=Header in output +pipeline.parameters.artic_illumina.samtool_filter2-6-flag.filter=Filter on bitwise flag +pipeline.parameters.artic_illumina.samtool_filter2-6-read_group=Select alignments from Read Group +#Tool Parameters - Tool: ivar_trim - Workflow Step #: 7 +#Wed Apr 07 10:26:30 SAST 2021 +pipeline.parameters.artic_illumina.ivar_trim-7-primer.cached_bed=Primer scheme name +pipeline.parameters.artic_illumina.ivar_trim-7-primer.source=Source of primer information +#Tool Parameters - Tool: qualimap_bamqc - Workflow Step #: 8 +#Wed Apr 07 10:26:30 SAST 2021 +pipeline.parameters.artic_illumina.qualimap_bamqc-8-plot_specific.homopolymer_size=Homopolymer size +pipeline.parameters.artic_illumina.qualimap_bamqc-8-plot_specific.n_bins=Number of bins to use in across-reference plots +pipeline.parameters.artic_illumina.qualimap_bamqc-8-plot_specific.paint_chromosome_limits=Draw chromosome limits +pipeline.parameters.artic_illumina.qualimap_bamqc-8-stats_regions.region_select=Reference genome regions to calculate mapping statistics for +#Tool Parameters - 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Tool: multiqc - Workflow Step #: 3 +#Wed Apr 07 10:26:30 SAST 2021 +pipeline.parameters.artic_illumina.multiqc-3-title=Report title +pipeline.parameters.artic_illumina.multiqc-3-comment=Custom comment +#Tool Parameters - Tool: bwa - Workflow Step #: 4 +#Wed Apr 07 10:26:30 SAST 2021 +pipeline.parameters.artic_illumina.bwa-4-reference_source.index_a=bwa-4-reference_source.index_a +pipeline.parameters.artic_illumina.bwa-4-fastq_input.iset_stats=Enter mean, standard deviation, max, and min for insert lengths. +pipeline.parameters.artic_illumina.bwa-4-analysis_type.analysis_type_selector=Select analysis mode +pipeline.parameters.artic_illumina.bwa-4-fastq_input.fastq_input_selector=Single or Paired-end reads +pipeline.parameters.artic_illumina.bwa-4-rg.rg_selector=bwa-4-rg.rg_selector +pipeline.parameters.artic_illumina.bwa-4-reference_source.reference_source_selector=bwa-4-reference_source.reference_source_selector +#Tool Parameters - Tool: picard - Workflow Step #: 5 +#Wed Apr 07 10:26:30 SAST 2021 +pipeline.parameters.artic_illumina.picard-5-duplicate_scoring_strategy=picard-5-duplicate_scoring_strategy +pipeline.parameters.artic_illumina.picard-5-validation_stringency=picard-5-validation_stringency +pipeline.parameters.artic_illumina.picard-5-barcode_tag=picard-5-barcode_tag +pipeline.parameters.artic_illumina.picard-5-read_name_regex=picard-5-read_name_regex +#Tool Parameters - Tool: samtool_filter2 - Workflow Step #: 6 +#Wed Apr 07 10:26:30 SAST 2021 +pipeline.parameters.artic_illumina.samtool_filter2-6-outputtype=Select the output format +pipeline.parameters.artic_illumina.samtool_filter2-6-regions=Select regions (only used when the input is in BAM format) +pipeline.parameters.artic_illumina.samtool_filter2-6-library=Select alignments from Library +pipeline.parameters.artic_illumina.samtool_filter2-6-header=Header in output +pipeline.parameters.artic_illumina.samtool_filter2-6-flag.filter=Filter on bitwise flag +pipeline.parameters.artic_illumina.samtool_filter2-6-read_group=Select alignments from Read Group +#Tool Parameters - Tool: ivar_trim - Workflow Step #: 7 +#Wed Apr 07 10:26:30 SAST 2021 +pipeline.parameters.artic_illumina.ivar_trim-7-primer.cached_bed=Primer scheme name +pipeline.parameters.artic_illumina.ivar_trim-7-primer.source=Source of primer information +#Tool Parameters - Tool: qualimap_bamqc - Workflow Step #: 8 +#Wed Apr 07 10:26:30 SAST 2021 +pipeline.parameters.artic_illumina.qualimap_bamqc-8-plot_specific.homopolymer_size=Homopolymer size +pipeline.parameters.artic_illumina.qualimap_bamqc-8-plot_specific.n_bins=Number of bins to use in across-reference plots +pipeline.parameters.artic_illumina.qualimap_bamqc-8-plot_specific.paint_chromosome_limits=Draw chromosome limits +pipeline.parameters.artic_illumina.qualimap_bamqc-8-stats_regions.region_select=Reference genome regions to calculate mapping statistics for +#Tool Parameters - 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+pipeline.parameters.artic_illumina.fastp-2-single_paired.adapter_trimming_options.adapter_sequence1=fastp-2-single_paired.adapter_trimming_options.adapter_sequence1 +pipeline.parameters.artic_illumina.fastp-2-read_mod_options.cutting_by_quality_options.cut_by_quality3=Cut by quality in tail (3') +pipeline.parameters.artic_illumina.fastp-2-read_mod_options.cutting_by_quality_options.cut_window_size=Cutting window size +pipeline.parameters.artic_illumina.fastp-2-single_paired.global_trimming_options.trim_tail1=fastp-2-single_paired.global_trimming_options.trim_tail1 +pipeline.parameters.artic_illumina.fastp-2-filter_options.length_filtering_options.length_required=Length required +pipeline.parameters.artic_illumina.fastp-2-output_options.report_json=Output JSON report +pipeline.parameters.artic_illumina.fastp-2-filter_options.quality_filtering_options.disable_quality_filtering=Disable quality filtering +pipeline.parameters.artic_illumina.fastp-2-output_options.report_html=Output HTML report +pipeline.parameters.artic_illumina.fastp-2-filter_options.quality_filtering_options.unqualified_percent_limit=Unqualified percent limit +pipeline.parameters.artic_illumina.fastp-2-single_paired.global_trimming_options.trim_tail2=fastp-2-single_paired.global_trimming_options.trim_tail2 +#Tool Parameters - Tool: multiqc - Workflow Step #: 3 +#Wed Apr 07 10:26:30 SAST 2021 +pipeline.parameters.artic_illumina.multiqc-3-title=Report title +pipeline.parameters.artic_illumina.multiqc-3-comment=Custom comment +#Tool Parameters - Tool: bwa - Workflow Step #: 4 +#Wed Apr 07 10:26:30 SAST 2021 +pipeline.parameters.artic_illumina.bwa-4-reference_source.index_a=bwa-4-reference_source.index_a +pipeline.parameters.artic_illumina.bwa-4-fastq_input.iset_stats=Enter mean, standard deviation, max, and min for insert lengths. +pipeline.parameters.artic_illumina.bwa-4-analysis_type.analysis_type_selector=Select analysis mode +pipeline.parameters.artic_illumina.bwa-4-fastq_input.fastq_input_selector=Single or Paired-end reads +pipeline.parameters.artic_illumina.bwa-4-rg.rg_selector=bwa-4-rg.rg_selector +pipeline.parameters.artic_illumina.bwa-4-reference_source.reference_source_selector=bwa-4-reference_source.reference_source_selector +#Tool Parameters - Tool: picard - Workflow Step #: 5 +#Wed Apr 07 10:26:30 SAST 2021 +pipeline.parameters.artic_illumina.picard-5-duplicate_scoring_strategy=picard-5-duplicate_scoring_strategy +pipeline.parameters.artic_illumina.picard-5-validation_stringency=picard-5-validation_stringency +pipeline.parameters.artic_illumina.picard-5-barcode_tag=picard-5-barcode_tag +pipeline.parameters.artic_illumina.picard-5-read_name_regex=picard-5-read_name_regex +#Tool Parameters - Tool: samtool_filter2 - Workflow Step #: 6 +#Wed Apr 07 10:26:30 SAST 2021 +pipeline.parameters.artic_illumina.samtool_filter2-6-outputtype=Select the output format +pipeline.parameters.artic_illumina.samtool_filter2-6-regions=Select regions (only used when the input is in BAM format) +pipeline.parameters.artic_illumina.samtool_filter2-6-library=Select alignments from Library +pipeline.parameters.artic_illumina.samtool_filter2-6-header=Header in output +pipeline.parameters.artic_illumina.samtool_filter2-6-flag.filter=Filter on bitwise flag +pipeline.parameters.artic_illumina.samtool_filter2-6-read_group=Select alignments from Read Group +#Tool Parameters - Tool: ivar_trim - Workflow Step #: 7 +#Wed Apr 07 10:26:30 SAST 2021 +pipeline.parameters.artic_illumina.ivar_trim-7-primer.cached_bed=Primer scheme name +pipeline.parameters.artic_illumina.ivar_trim-7-primer.source=Source of primer information +#Tool Parameters - Tool: qualimap_bamqc - Workflow Step #: 8 +#Wed Apr 07 10:26:30 SAST 2021 +pipeline.parameters.artic_illumina.qualimap_bamqc-8-plot_specific.homopolymer_size=Homopolymer size 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Apr 07 10:26:30 SAST 2021 +pipeline.parameters.artic_illumina.bwa-4-reference_source.index_a=bwa-4-reference_source.index_a +pipeline.parameters.artic_illumina.bwa-4-fastq_input.iset_stats=Enter mean, standard deviation, max, and min for insert lengths. +pipeline.parameters.artic_illumina.bwa-4-analysis_type.analysis_type_selector=Select analysis mode +pipeline.parameters.artic_illumina.bwa-4-fastq_input.fastq_input_selector=Single or Paired-end reads +pipeline.parameters.artic_illumina.bwa-4-rg.rg_selector=bwa-4-rg.rg_selector +pipeline.parameters.artic_illumina.bwa-4-reference_source.reference_source_selector=bwa-4-reference_source.reference_source_selector +#Tool Parameters - Tool: picard - Workflow Step #: 5 +#Wed Apr 07 10:26:30 SAST 2021 +pipeline.parameters.artic_illumina.picard-5-duplicate_scoring_strategy=picard-5-duplicate_scoring_strategy +pipeline.parameters.artic_illumina.picard-5-validation_stringency=picard-5-validation_stringency 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name +pipeline.parameters.artic_illumina.ivar_trim-7-primer.source=Source of primer information +#Tool Parameters - Tool: qualimap_bamqc - Workflow Step #: 8 +#Wed Apr 07 10:26:30 SAST 2021 +pipeline.parameters.artic_illumina.qualimap_bamqc-8-plot_specific.homopolymer_size=Homopolymer size +pipeline.parameters.artic_illumina.qualimap_bamqc-8-plot_specific.n_bins=Number of bins to use in across-reference plots +pipeline.parameters.artic_illumina.qualimap_bamqc-8-plot_specific.paint_chromosome_limits=Draw chromosome limits +pipeline.parameters.artic_illumina.qualimap_bamqc-8-stats_regions.region_select=Reference genome regions to calculate mapping statistics for +#Tool Parameters - Tool: multiqc - Workflow Step #: 11 +#Wed Apr 07 10:26:30 SAST 2021 +pipeline.parameters.artic_illumina.multiqc-11-title=Report title +pipeline.parameters.artic_illumina.multiqc-11-comment=Custom comment +#Tool Parameters - Tool: qc - Workflow Step #: 12 +#Wed Apr 07 10:26:30 SAST 2021 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Workflow Step #: 2 +#Thu Aug 26 14:05:27 SAST 2021 +pipeline.parameters.artic_illumina.fastp-2-overrepresented_sequence_analysis.overrepresentation_analysis=Enable overrepresented analysis +pipeline.parameters.artic_illumina.fastp-2-filter_options.length_filtering_options.disable_length_filtering=Disable length filtering +pipeline.parameters.artic_illumina.fastp-2-read_mod_options.umi_processing.umi_loc=UMI location +pipeline.parameters.artic_illumina.fastp-2-single_paired.adapter_trimming_options.disable_adapter_trimming=fastp-2-single_paired.adapter_trimming_options.disable_adapter_trimming +pipeline.parameters.artic_illumina.fastp-2-single_paired.adapter_trimming_options.adapter_sequence2=fastp-2-single_paired.adapter_trimming_options.adapter_sequence2 +pipeline.parameters.artic_illumina.fastp-2-read_mod_options.base_correction_options.correction=Enable base correction +pipeline.parameters.artic_illumina.fastp-2-read_mod_options.umi_processing.umi_prefix=UMI prefix +pipeline.parameters.artic_illumina.fastp-2-read_mod_options.polyx_tail_trimming.polyx_trimming_select=PolyX tail trimming +pipeline.parameters.artic_illumina.fastp-2-read_mod_options.cutting_by_quality_options.cut_by_quality5=Cut by quality in front (5') +pipeline.parameters.artic_illumina.fastp-2-single_paired.adapter_trimming_options.adapter_sequence1=fastp-2-single_paired.adapter_trimming_options.adapter_sequence1 +pipeline.parameters.artic_illumina.fastp-2-read_mod_options.cutting_by_quality_options.cut_by_quality3=Cut by quality in tail (3') +pipeline.parameters.artic_illumina.fastp-2-filter_options.low_complexity_filter.enable_low_complexity_filter=Enable low complexity filter +pipeline.parameters.artic_illumina.fastp-2-single_paired.single_paired_selector=Single-end or paired reads +pipeline.parameters.artic_illumina.fastp-2-read_mod_options.polyg_tail_trimming.trimming_select=PolyG tail trimming +pipeline.parameters.artic_illumina.fastp-2-output_options.report_json=Output JSON report +pipeline.parameters.artic_illumina.fastp-2-filter_options.quality_filtering_options.disable_quality_filtering=Disable quality filtering +pipeline.parameters.artic_illumina.fastp-2-output_options.report_html=Output HTML report +pipeline.parameters.artic_illumina.fastp-2-read_mod_options.umi_processing.umi=Enable unique molecular identifer +#Tool Parameters - Tool: multiqc - Workflow Step #: 3 +#Thu Aug 26 14:05:27 SAST 2021 +pipeline.parameters.artic_illumina.multiqc-3-title=Report title +pipeline.parameters.artic_illumina.multiqc-3-comment=Custom comment +#Tool Parameters - Tool: bwa - Workflow Step #: 4 +#Thu Aug 26 14:05:27 SAST 2021 +pipeline.parameters.artic_illumina.bwa-4-reference_source.index_a=bwa-4-reference_source.index_a +pipeline.parameters.artic_illumina.bwa-4-fastq_input.iset_stats=Enter mean, standard deviation, max, and min for insert lengths. +pipeline.parameters.artic_illumina.bwa-4-analysis_type.analysis_type_selector=Select analysis mode +pipeline.parameters.artic_illumina.bwa-4-fastq_input.fastq_input_selector=Single or Paired-end reads +pipeline.parameters.artic_illumina.bwa-4-rg.rg_selector=bwa-4-rg.rg_selector +pipeline.parameters.artic_illumina.bwa-4-reference_source.reference_source_selector=bwa-4-reference_source.reference_source_selector +#Tool Parameters - Tool: picard - Workflow Step #: 5 +#Thu Aug 26 14:05:27 SAST 2021 +pipeline.parameters.artic_illumina.picard-5-duplicate_scoring_strategy=picard-5-duplicate_scoring_strategy +pipeline.parameters.artic_illumina.picard-5-validation_stringency=picard-5-validation_stringency +pipeline.parameters.artic_illumina.picard-5-barcode_tag=picard-5-barcode_tag +pipeline.parameters.artic_illumina.picard-5-read_name_regex=picard-5-read_name_regex +#Tool Parameters - Tool: samtools_view - Workflow Step #: 6 +#Thu Aug 26 14:05:27 SAST 2021 +pipeline.parameters.artic_illumina.samtools_view-6-mode.filter_config.quality=samtools_view-6-mode.filter_config.quality +pipeline.parameters.artic_illumina.samtools_view-6-mode.outtype=samtools_view-6-mode.outtype +pipeline.parameters.artic_illumina.samtools_view-6-mode.filter_config.cond_rg.select_rg=samtools_view-6-mode.filter_config.cond_rg.select_rg +pipeline.parameters.artic_illumina.samtools_view-6-mode.output_options.adv_output.collapsecigar=samtools_view-6-mode.output_options.adv_output.collapsecigar +pipeline.parameters.artic_illumina.samtools_view-6-addref_cond.addref_select=samtools_view-6-addref_cond.addref_select +pipeline.parameters.artic_illumina.samtools_view-6-mode.subsample_config.subsampling_mode.select_subsample=samtools_view-6-mode.subsample_config.subsampling_mode.select_subsample +pipeline.parameters.artic_illumina.samtools_view-6-mode.output_options.output_format.oformat=samtools_view-6-mode.output_options.output_format.oformat +pipeline.parameters.artic_illumina.samtools_view-6-mode.subsample_config.subsampling_mode.factor=samtools_view-6-mode.subsample_config.subsampling_mode.factor +pipeline.parameters.artic_illumina.samtools_view-6-mode.filter_config.cond_region.select_region=samtools_view-6-mode.filter_config.cond_region.select_region +pipeline.parameters.artic_illumina.samtools_view-6-mode.filter_config.library=samtools_view-6-mode.filter_config.library +pipeline.parameters.artic_illumina.samtools_view-6-mode.output_options.reads_report_type=samtools_view-6-mode.output_options.reads_report_type +pipeline.parameters.artic_illumina.samtools_view-6-mode.output_options.complementary_output=samtools_view-6-mode.output_options.complementary_output +#Tool Parameters - Tool: ivar_trim - Workflow Step #: 7 +#Thu Aug 26 14:05:27 SAST 2021 +pipeline.parameters.artic_illumina.ivar_trim-7-amplicons.filter_by=Filter reads based on amplicon info +pipeline.parameters.artic_illumina.ivar_trim-7-primer.cached_bed=Primer scheme name +pipeline.parameters.artic_illumina.ivar_trim-7-primer.source=Source of primer information +#Tool Parameters - Tool: qualimap_bamqc - Workflow Step #: 8 +#Thu Aug 26 14:05:27 SAST 2021 +pipeline.parameters.artic_illumina.qualimap_bamqc-8-plot_specific.homopolymer_size=Homopolymer size +pipeline.parameters.artic_illumina.qualimap_bamqc-8-plot_specific.n_bins=Number of bins to use in across-reference plots +pipeline.parameters.artic_illumina.qualimap_bamqc-8-plot_specific.paint_chromosome_limits=Draw chromosome limits +pipeline.parameters.artic_illumina.qualimap_bamqc-8-stats_regions.region_select=Reference genome regions to calculate mapping statistics for +#Tool Parameters - Tool: ivar_variants - Workflow Step #: 9 +#Thu Aug 26 14:05:27 SAST 2021 +pipeline.parameters.artic_illumina.ivar_variants-9-output_format.choice=Output format +pipeline.parameters.artic_illumina.ivar_variants-9-output_format.pass_only=In VCF only output variants that PASS all filters +#Tool Parameters - Tool: multiqc - Workflow Step #: 11 +#Thu Aug 26 14:05:27 SAST 2021 +pipeline.parameters.artic_illumina.multiqc-11-title=Report title +pipeline.parameters.artic_illumina.multiqc-11-comment=Custom comment +#Tool Parameters - Tool: qc - Workflow Step #: 12 +#Thu Aug 26 14:05:27 SAST 2021 +pipeline.parameters.artic_illumina.qc-12-qc_type_conditional.qc_type=Input Type +#Tool Parameters - Tool: text_processing - Workflow Step #: 13 +#Thu Aug 26 14:05:27 SAST 2021 +pipeline.parameters.artic_illumina.text_processing-13-code=AWK Program +pipeline.parameters.artic_illumina.text_processing-13-adv_opts.adv_opts_selector=text_processing-13-adv_opts.adv_opts_selector +#Tool Parameters - Tool: pangolin - Workflow Step #: 14 +#Thu Aug 26 14:05:27 SAST 2021 +pipeline.parameters.artic_illumina.pangolin-14-db.source=pangoLEARN source +#Tool Parameters - Tool: nextclade - Workflow Step #: 15 +#Thu Aug 26 14:05:27 SAST 2021 +pipeline.parameters.artic_illumina.nextclade-15-adv.advanced_options=nextclade-15-adv.advanced_options diff --git a/compose/irida/tmp/workflows/0.1.9/irida_workflow.xml b/compose/irida/tmp/workflows/0.1.9/irida_workflow.xml new file mode 100644 index 000000000..4115741a0 --- /dev/null +++ b/compose/irida/tmp/workflows/0.1.9/irida_workflow.xml @@ -0,0 +1,128 @@ + + + fe8bfdc1-bf00-49e0-bfbd-7c0f9f0c926e + Artic_Illumina + 0.1.9 + ARTICILLUMINA_PIPELINE + + sequence_reads_list_paired + reference + true + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + nextclade + iuc + https://toolshed.g2.bx.psu.edu + b74b9a7b3e3b + + + ivar_variants + iuc + https://toolshed.g2.bx.psu.edu + aea7008fe1f1 + + + pangolin + iuc + https://toolshed.g2.bx.psu.edu + debfccc4d65b + + + fastp + iuc + https://toolshed.g2.bx.psu.edu + dbf9c561ef29 + + + text_processing + bgruening + https://toolshed.g2.bx.psu.edu + fb4ff3c42cd3 + + + picard + devteam + https://toolshed.g2.bx.psu.edu + 7d34178f2812 + + + bwa + devteam + https://toolshed.g2.bx.psu.edu + 64f11cf59c6e + + + qc + sanbi-uwc + https://testtoolshed.g2.bx.psu.edu + 6bdec8c62aec + + + samtools_view + iuc + https://toolshed.g2.bx.psu.edu + b72793637686 + + + multiqc + iuc + https://toolshed.g2.bx.psu.edu + 75c93c70d094 + + + qualimap_bamqc + iuc + https://toolshed.g2.bx.psu.edu + e7fd6754d093 + + + ivar_consensus + iuc + https://toolshed.g2.bx.psu.edu + 2d9926ce62be + + + ivar_trim + iuc + https://toolshed.g2.bx.psu.edu + c092052ed673 + + + diff --git a/compose/irida/tmp/workflows/0.1.9/irida_workflow_structure.ga b/compose/irida/tmp/workflows/0.1.9/irida_workflow_structure.ga new file mode 100644 index 000000000..c4c058528 --- /dev/null +++ b/compose/irida/tmp/workflows/0.1.9/irida_workflow_structure.ga @@ -0,0 +1,904 @@ +{ + "a_galaxy_workflow" : "true", + "annotation" : "Workflow for generating SARS-Cov2 consensus and variants from viral amplicon data. 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+ "version" : 1 +} \ No newline at end of file diff --git a/compose/irida/tmp/workflows/0.1.9/messages_en.properties b/compose/irida/tmp/workflows/0.1.9/messages_en.properties new file mode 100644 index 000000000..86168e7f0 --- /dev/null +++ b/compose/irida/tmp/workflows/0.1.9/messages_en.properties @@ -0,0 +1,97 @@ +#Pipeline Info Properties +#Thu Aug 26 14:05:27 SAST 2021 +workflow.ARTICILLUMINA_PIPELINE.description=Workflow for generating SARS-Cov2 consensus and variants from viral amplicon data.\nUses iVar toolsuite. +pipeline.h1.Artic_Illumina=SARS-CoV-2 Artic Illumina Pipeline +pipeline.parameters.modal-title.artic_illumina=SARS-CoV-2 Artic Illumina Pipeline Parameters +workflow.label.share-analysis-samples.ARTICILLUMINA_PIPELINE=Save Results to Project Line List Metadata +pipeline.title.Artic_Illumina=Pipelines - SARS-CoV-2 Artic Illumina +workflow.ARTICILLUMINA_PIPELINE.title=SARS-CoV-2 Artic Illumina Pipeline +#Tool Parameters - Tool: fastp - Workflow Step #: 2 +#Thu Aug 26 14:05:27 SAST 2021 +pipeline.parameters.artic_illumina.fastp-2-overrepresented_sequence_analysis.overrepresentation_analysis=Enable overrepresented analysis +pipeline.parameters.artic_illumina.fastp-2-filter_options.length_filtering_options.disable_length_filtering=Disable length filtering +pipeline.parameters.artic_illumina.fastp-2-read_mod_options.umi_processing.umi_loc=UMI location +pipeline.parameters.artic_illumina.fastp-2-single_paired.adapter_trimming_options.disable_adapter_trimming=fastp-2-single_paired.adapter_trimming_options.disable_adapter_trimming +pipeline.parameters.artic_illumina.fastp-2-single_paired.adapter_trimming_options.adapter_sequence2=fastp-2-single_paired.adapter_trimming_options.adapter_sequence2 +pipeline.parameters.artic_illumina.fastp-2-read_mod_options.base_correction_options.correction=Enable base correction +pipeline.parameters.artic_illumina.fastp-2-read_mod_options.umi_processing.umi_prefix=UMI prefix +pipeline.parameters.artic_illumina.fastp-2-read_mod_options.polyx_tail_trimming.polyx_trimming_select=PolyX tail trimming +pipeline.parameters.artic_illumina.fastp-2-read_mod_options.cutting_by_quality_options.cut_by_quality5=Cut by quality in front (5') +pipeline.parameters.artic_illumina.fastp-2-single_paired.adapter_trimming_options.adapter_sequence1=fastp-2-single_paired.adapter_trimming_options.adapter_sequence1 +pipeline.parameters.artic_illumina.fastp-2-read_mod_options.cutting_by_quality_options.cut_by_quality3=Cut by quality in tail (3') +pipeline.parameters.artic_illumina.fastp-2-filter_options.low_complexity_filter.enable_low_complexity_filter=Enable low complexity filter +pipeline.parameters.artic_illumina.fastp-2-single_paired.single_paired_selector=Single-end or paired reads +pipeline.parameters.artic_illumina.fastp-2-read_mod_options.polyg_tail_trimming.trimming_select=PolyG tail trimming +pipeline.parameters.artic_illumina.fastp-2-output_options.report_json=Output JSON report +pipeline.parameters.artic_illumina.fastp-2-filter_options.quality_filtering_options.disable_quality_filtering=Disable quality filtering +pipeline.parameters.artic_illumina.fastp-2-output_options.report_html=Output HTML report +pipeline.parameters.artic_illumina.fastp-2-read_mod_options.umi_processing.umi=Enable unique molecular identifer +#Tool Parameters - Tool: multiqc - Workflow Step #: 3 +#Thu Aug 26 14:05:27 SAST 2021 +pipeline.parameters.artic_illumina.multiqc-3-title=Report title +pipeline.parameters.artic_illumina.multiqc-3-comment=Custom comment +#Tool Parameters - Tool: bwa - Workflow Step #: 4 +#Thu Aug 26 14:05:27 SAST 2021 +pipeline.parameters.artic_illumina.bwa-4-reference_source.index_a=bwa-4-reference_source.index_a +pipeline.parameters.artic_illumina.bwa-4-fastq_input.iset_stats=Enter mean, standard deviation, max, and min for insert lengths. +pipeline.parameters.artic_illumina.bwa-4-analysis_type.analysis_type_selector=Select analysis mode +pipeline.parameters.artic_illumina.bwa-4-fastq_input.fastq_input_selector=Single or Paired-end reads +pipeline.parameters.artic_illumina.bwa-4-rg.rg_selector=bwa-4-rg.rg_selector +pipeline.parameters.artic_illumina.bwa-4-reference_source.reference_source_selector=bwa-4-reference_source.reference_source_selector +#Tool Parameters - Tool: picard - Workflow Step #: 5 +#Thu Aug 26 14:05:27 SAST 2021 +pipeline.parameters.artic_illumina.picard-5-duplicate_scoring_strategy=picard-5-duplicate_scoring_strategy +pipeline.parameters.artic_illumina.picard-5-validation_stringency=picard-5-validation_stringency +pipeline.parameters.artic_illumina.picard-5-barcode_tag=picard-5-barcode_tag +pipeline.parameters.artic_illumina.picard-5-read_name_regex=picard-5-read_name_regex +#Tool Parameters - Tool: samtools_view - Workflow Step #: 6 +#Thu Aug 26 14:05:27 SAST 2021 +pipeline.parameters.artic_illumina.samtools_view-6-mode.filter_config.quality=samtools_view-6-mode.filter_config.quality +pipeline.parameters.artic_illumina.samtools_view-6-mode.outtype=samtools_view-6-mode.outtype +pipeline.parameters.artic_illumina.samtools_view-6-mode.filter_config.cond_rg.select_rg=samtools_view-6-mode.filter_config.cond_rg.select_rg +pipeline.parameters.artic_illumina.samtools_view-6-mode.output_options.adv_output.collapsecigar=samtools_view-6-mode.output_options.adv_output.collapsecigar +pipeline.parameters.artic_illumina.samtools_view-6-addref_cond.addref_select=samtools_view-6-addref_cond.addref_select +pipeline.parameters.artic_illumina.samtools_view-6-mode.subsample_config.subsampling_mode.select_subsample=samtools_view-6-mode.subsample_config.subsampling_mode.select_subsample +pipeline.parameters.artic_illumina.samtools_view-6-mode.output_options.output_format.oformat=samtools_view-6-mode.output_options.output_format.oformat +pipeline.parameters.artic_illumina.samtools_view-6-mode.subsample_config.subsampling_mode.factor=samtools_view-6-mode.subsample_config.subsampling_mode.factor +pipeline.parameters.artic_illumina.samtools_view-6-mode.filter_config.cond_region.select_region=samtools_view-6-mode.filter_config.cond_region.select_region +pipeline.parameters.artic_illumina.samtools_view-6-mode.filter_config.library=samtools_view-6-mode.filter_config.library +pipeline.parameters.artic_illumina.samtools_view-6-mode.output_options.reads_report_type=samtools_view-6-mode.output_options.reads_report_type +pipeline.parameters.artic_illumina.samtools_view-6-mode.output_options.complementary_output=samtools_view-6-mode.output_options.complementary_output +#Tool Parameters - Tool: ivar_trim - Workflow Step #: 7 +#Thu Aug 26 14:05:27 SAST 2021 +pipeline.parameters.artic_illumina.ivar_trim-7-amplicons.filter_by=Filter reads based on amplicon info +pipeline.parameters.artic_illumina.ivar_trim-7-primer.cached_bed=Primer scheme name +pipeline.parameters.artic_illumina.ivar_trim-7-primer.source=Source of primer information +#Tool Parameters - Tool: qualimap_bamqc - Workflow Step #: 8 +#Thu Aug 26 14:05:27 SAST 2021 +pipeline.parameters.artic_illumina.qualimap_bamqc-8-plot_specific.homopolymer_size=Homopolymer size +pipeline.parameters.artic_illumina.qualimap_bamqc-8-plot_specific.n_bins=Number of bins to use in across-reference plots +pipeline.parameters.artic_illumina.qualimap_bamqc-8-plot_specific.paint_chromosome_limits=Draw chromosome limits +pipeline.parameters.artic_illumina.qualimap_bamqc-8-stats_regions.region_select=Reference genome regions to calculate mapping statistics for +#Tool Parameters - Tool: ivar_variants - Workflow Step #: 9 +#Thu Aug 26 14:05:27 SAST 2021 +pipeline.parameters.artic_illumina.ivar_variants-9-output_format.choice=Output format +pipeline.parameters.artic_illumina.ivar_variants-9-output_format.pass_only=In VCF only output variants that PASS all filters +pipeline.parameters.artic_illumina.ivar_variants-9-min_qual=Minimum quality score threshold to count base +pipeline.parameters.artic_illumina.ivar_variants-9-min_freq=Minimum frequency threshold for variants +#Tool Parameters - Tool: multiqc - Workflow Step #: 11 +#Thu Aug 26 14:05:27 SAST 2021 +pipeline.parameters.artic_illumina.multiqc-11-title=Report title +pipeline.parameters.artic_illumina.multiqc-11-comment=Custom comment +#Tool Parameters - Tool: qc - Workflow Step #: 12 +#Thu Aug 26 14:05:27 SAST 2021 +pipeline.parameters.artic_illumina.qc-12-qc_type_conditional.qc_type=Input Type +#Tool Parameters - Tool: text_processing - Workflow Step #: 13 +#Thu Aug 26 14:05:27 SAST 2021 +pipeline.parameters.artic_illumina.text_processing-13-code=AWK Program +pipeline.parameters.artic_illumina.text_processing-13-adv_opts.adv_opts_selector=text_processing-13-adv_opts.adv_opts_selector +#Tool Parameters - Tool: pangolin - Workflow Step #: 14 +#Thu Aug 26 14:05:27 SAST 2021 +pipeline.parameters.artic_illumina.pangolin-14-db.source=pangoLEARN source +#Tool Parameters - Tool: nextclade - Workflow Step #: 15 +#Thu Aug 26 14:05:27 SAST 2021 +pipeline.parameters.artic_illumina.nextclade-15-adv.advanced_options=nextclade-15-adv.advanced_options +# ivar_consensus +pipeline.parameters.artic_illumina.ivar_consensus-16-min_qual=Minimum quality score threshold to count base +pipeline.parameters.artic_illumina.ivar_consensus-16-min_freq=Minimum frequency threshold for variants diff --git a/compose/irida/tmp/workflows/0.1.9/tools.yaml b/compose/irida/tmp/workflows/0.1.9/tools.yaml new file mode 100644 index 000000000..0ba5a3211 --- /dev/null +++ b/compose/irida/tmp/workflows/0.1.9/tools.yaml @@ -0,0 +1,83 @@ +install_tool_dependencies: True +install_repository_dependencies: True +install_resolver_dependencies: True + +tools: +- name: ivar_variants + owner: iuc + revisions: + - 3888bbe7a9ca + tool_panel_section_label: Tools from workflows + tool_shed_url: https://toolshed.g2.bx.psu.edu/ +- name: multiqc + owner: iuc + revisions: + - 75c93c70d094 + tool_panel_section_label: Tools from workflows + tool_shed_url: https://toolshed.g2.bx.psu.edu/ +- name: bwa + owner: devteam + revisions: + - 64f11cf59c6e + tool_panel_section_label: Tools from workflows + tool_shed_url: https://toolshed.g2.bx.psu.edu/ +- name: qualimap_bamqc + owner: iuc + revisions: + - e7fd6754d093 + tool_panel_section_label: Tools from workflows + tool_shed_url: https://toolshed.g2.bx.psu.edu/ +- name: pangolin + owner: iuc + revisions: + - debfccc4d65b + tool_panel_section_label: Tools from workflows + tool_shed_url: https://toolshed.g2.bx.psu.edu/ +- name: nextclade + owner: iuc + revisions: + - b74b9a7b3e3b + tool_panel_section_label: Tools from workflows + tool_shed_url: https://toolshed.g2.bx.psu.edu/ +- name: ivar_trim + owner: iuc + revisions: + - c092052ed673 + tool_panel_section_label: Tools from workflows + tool_shed_url: https://toolshed.g2.bx.psu.edu/ +- name: picard + owner: devteam + revisions: + - 7d34178f2812 + tool_panel_section_label: Tools from workflows + tool_shed_url: https://toolshed.g2.bx.psu.edu/ +- name: qc + owner: sanbi-uwc + revisions: + - 6bdec8c62aec + tool_panel_section_label: Tools from workflows + tool_shed_url: https://testtoolshed.g2.bx.psu.edu/ +- name: text_processing + owner: bgruening + revisions: + - 9ff72e942410 + tool_panel_section_label: Tools from workflows + tool_shed_url: https://toolshed.g2.bx.psu.edu/ +- name: samtools_view + owner: iuc + revisions: + - b72793637686 + tool_panel_section_label: Tools from workflows + tool_shed_url: https://toolshed.g2.bx.psu.edu/ +- name: fastp + owner: iuc + revisions: + - dbf9c561ef29 + tool_panel_section_label: Tools from workflows + tool_shed_url: https://toolshed.g2.bx.psu.edu/ +- name: ivar_consensus + owner: iuc + revisions: + - 731182d54f78 + tool_panel_section_label: Tools from workflows + tool_shed_url: https://toolshed.g2.bx.psu.edu/ diff --git a/compose/irida/wait-for-it.sh b/compose/irida/wait-for-it.sh new file mode 100755 index 000000000..401a6f179 --- /dev/null +++ b/compose/irida/wait-for-it.sh @@ -0,0 +1,177 @@ +#!/usr/bin/env bash +# Use this script to test if a given TCP host/port are available + +cmdname=$(basename $0) + +echoerr() { if [[ $QUIET -ne 1 ]]; then echo "$@" 1>&2; fi } + +usage() +{ + cat << USAGE >&2 +Usage: + $cmdname host:port [-s] [-t timeout] [-- command args] + -h HOST | --host=HOST Host or IP under test + -p PORT | --port=PORT TCP port under test + Alternatively, you specify the host and port as host:port + -s | --strict Only execute subcommand if the test succeeds + -q | --quiet Don't output any status messages + -t TIMEOUT | --timeout=TIMEOUT + Timeout in seconds, zero for no timeout + -- COMMAND ARGS Execute command with args after the test finishes +USAGE + exit 1 +} + +wait_for() +{ + if [[ $TIMEOUT -gt 0 ]]; then + echoerr "$cmdname: waiting $TIMEOUT seconds for $HOST:$PORT" + else + echoerr "$cmdname: waiting for $HOST:$PORT without a timeout" + fi + start_ts=$(date +%s) + while : + do + if [[ $ISBUSY -eq 1 ]]; then + nc -z $HOST $PORT + result=$? + else + (echo > /dev/tcp/$HOST/$PORT) >/dev/null 2>&1 + result=$? + fi + if [[ $result -eq 0 ]]; then + end_ts=$(date +%s) + echoerr "$cmdname: $HOST:$PORT is available after $((end_ts - start_ts)) seconds" + break + fi + sleep 1 + done + return $result +} + +wait_for_wrapper() +{ + # In order to support SIGINT during timeout: http://unix.stackexchange.com/a/57692 + if [[ $QUIET -eq 1 ]]; then + timeout $BUSYTIMEFLAG $TIMEOUT $0 --quiet --child --host=$HOST --port=$PORT --timeout=$TIMEOUT & + else + timeout $BUSYTIMEFLAG $TIMEOUT $0 --child --host=$HOST --port=$PORT --timeout=$TIMEOUT & + fi + PID=$! + trap "kill -INT -$PID" INT + wait $PID + RESULT=$? + if [[ $RESULT -ne 0 ]]; then + echoerr "$cmdname: timeout occurred after waiting $TIMEOUT seconds for $HOST:$PORT" + fi + return $RESULT +} + +# process arguments +while [[ $# -gt 0 ]] +do + case "$1" in + *:* ) + hostport=(${1//:/ }) + HOST=${hostport[0]} + PORT=${hostport[1]} + shift 1 + ;; + --child) + CHILD=1 + shift 1 + ;; + -q | --quiet) + QUIET=1 + shift 1 + ;; + -s | --strict) + STRICT=1 + shift 1 + ;; + -h) + HOST="$2" + if [[ $HOST == "" ]]; then break; fi + shift 2 + ;; + --host=*) + HOST="${1#*=}" + shift 1 + ;; + -p) + PORT="$2" + if [[ $PORT == "" ]]; then break; fi + shift 2 + ;; + --port=*) + PORT="${1#*=}" + shift 1 + ;; + -t) + TIMEOUT="$2" + if [[ $TIMEOUT == "" ]]; then break; fi + shift 2 + ;; + --timeout=*) + TIMEOUT="${1#*=}" + shift 1 + ;; + --) + shift + CLI="$@" + break + ;; + --help) + usage + ;; + *) + echoerr "Unknown argument: $1" + usage + ;; + esac +done + +if [[ "$HOST" == "" || "$PORT" == "" ]]; then + echoerr "Error: you need to provide a host and port to test." + usage +fi + +TIMEOUT=${TIMEOUT:-15} +STRICT=${STRICT:-0} +CHILD=${CHILD:-0} +QUIET=${QUIET:-0} + +# check to see if timeout is from busybox? +# check to see if timeout is from busybox? +TIMEOUT_PATH=$(realpath $(which timeout)) +if [[ $TIMEOUT_PATH =~ "busybox" ]]; then + ISBUSY=1 + BUSYTIMEFLAG="-t" +else + ISBUSY=0 + BUSYTIMEFLAG="" +fi + +if [[ $CHILD -gt 0 ]]; then + wait_for + RESULT=$? + exit $RESULT +else + if [[ $TIMEOUT -gt 0 ]]; then + wait_for_wrapper + RESULT=$? + else + wait_for + RESULT=$? + fi +fi + +if [[ $CLI != "" ]]; then + if [[ $RESULT -ne 0 && $STRICT -eq 1 ]]; then + echoerr "$cmdname: strict mode, refusing to execute subprocess" + exit $RESULT + fi + exec $CLI +else + exit $RESULT +fi diff --git a/compose/irida/web.conf b/compose/irida/web.conf new file mode 100644 index 000000000..453782807 --- /dev/null +++ b/compose/irida/web.conf @@ -0,0 +1,24 @@ +# The externally visible URL for accessing this instance of IRIDA. 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z^o|OU2>f*)i$~-%3sK7SVAT1Ni}fQEeZ)ti2eC+t2#B#Ui-|a`AS*mlV=jYhQ~?rk zi>-LH*VbhYsqof6H>}=yp)O&2!w#viG_l3k?+nO0F-xRCjRWmN-F`5v$t26#HIZeR zc1M<9loV(l`96XXcP`l$7Y-tn_Z2Mc*k*jftTA`KPXcRkf=~$)8LaTbq?w@>9s}4m zDK*4LK~hp+UR^&1JWzgb539+(DMETqg3 z1O3c!Ky2v4g@Mo1uH7^ngpQ=QgJ}t9;sQY?MClae9yGrmH#U2Hg@~3@V_YSobnaHs zqLmi@VYvs3{bp<%amv1yPeK|CnlJNQLYo3N?%@eZKK8!dvFeA3StO~QGJATo)+(vxAmI8?R7&pE_MWi~JCdx8E0G#mSzaPi{OTu5Vy`Sp-*Mk7?!Y};J_7BkV zZppZ%4v-(bx@g-!m?!u|s|lV9!5A>%NQr=SkOZAn5;W(jOfj{0F{&f};O3_iwQ1e`-D9 zuYc$MSGV{lNculB{|1x($-MR7ng13B?XMd78*KWgChqrM`HPu{TXQJr(rg5f716!ojlU$G`Xb(X)6%>OHA z{6wDoYTvKukDvCnBL2Vo Date: Mon, 15 Nov 2021 14:30:09 +0000 Subject: [PATCH 02/36] Add scripts for configuring IRIDA (WIP) --- compose/galaxy_tools.yml | 88 +++++++++++++++++++++ compose/update_plugins_and_tools.py | 114 ++++++++++++++++++++++++++++ compose/workflows.txt | 2 + 3 files changed, 204 insertions(+) create mode 100644 compose/galaxy_tools.yml create mode 100644 compose/update_plugins_and_tools.py create mode 100644 compose/workflows.txt diff --git a/compose/galaxy_tools.yml b/compose/galaxy_tools.yml new file mode 100644 index 000000000..5c98a3dd9 --- /dev/null +++ b/compose/galaxy_tools.yml @@ -0,0 +1,88 @@ +install_repository_dependencies: true +install_resolver_dependencies: true +install_tool_dependencies: true +tools: +- name: data_manager_primer_scheme_bedfiles + owner: iuc + revisions: + - 157a5c9ea72a + tool_panel_section_label: COMBAT-SARS-COV-2::ARTIC-MINION + tool_shed_url: toolshed.g2.bx.psu.edu +- name: ivar_variants + owner: iuc + revisions: + - 3888bbe7a9ca + tool_panel_section_label: Tools from workflows + tool_shed_url: https://toolshed.g2.bx.psu.edu/ +- name: multiqc + owner: iuc + revisions: + - 75c93c70d094 + tool_panel_section_label: Tools from workflows + tool_shed_url: https://toolshed.g2.bx.psu.edu/ +- name: bwa + owner: devteam + revisions: + - 64f11cf59c6e + tool_panel_section_label: Tools from workflows + tool_shed_url: https://toolshed.g2.bx.psu.edu/ +- name: qualimap_bamqc + owner: iuc + revisions: + - e7fd6754d093 + tool_panel_section_label: Tools from workflows + tool_shed_url: https://toolshed.g2.bx.psu.edu/ +- name: pangolin + owner: iuc + revisions: + - debfccc4d65b + tool_panel_section_label: Tools from workflows + tool_shed_url: https://toolshed.g2.bx.psu.edu/ +- name: nextclade + owner: iuc + revisions: + - b74b9a7b3e3b + tool_panel_section_label: Tools from workflows + tool_shed_url: https://toolshed.g2.bx.psu.edu/ +- name: ivar_trim + owner: iuc + revisions: + - c092052ed673 + tool_panel_section_label: Tools from workflows + tool_shed_url: https://toolshed.g2.bx.psu.edu/ +- name: picard + owner: devteam + revisions: + - 7d34178f2812 + tool_panel_section_label: Tools from workflows + tool_shed_url: https://toolshed.g2.bx.psu.edu/ +- name: qc + owner: sanbi-uwc + revisions: + - 6bdec8c62aec + tool_panel_section_label: Tools from workflows + tool_shed_url: https://testtoolshed.g2.bx.psu.edu/ +- name: text_processing + owner: bgruening + revisions: + - 9ff72e942410 + tool_panel_section_label: Tools from workflows + tool_shed_url: https://toolshed.g2.bx.psu.edu/ +- name: samtools_view + owner: iuc + revisions: + - b72793637686 + tool_panel_section_label: Tools from workflows + tool_shed_url: https://toolshed.g2.bx.psu.edu/ +- name: fastp + owner: iuc + revisions: + - dbf9c561ef29 + tool_panel_section_label: Tools from workflows + tool_shed_url: https://toolshed.g2.bx.psu.edu/ +- name: ivar_consensus + owner: iuc + revisions: + - 731182d54f78 + tool_panel_section_label: Tools from workflows + tool_shed_url: https://toolshed.g2.bx.psu.edu/ diff --git a/compose/update_plugins_and_tools.py b/compose/update_plugins_and_tools.py new file mode 100644 index 000000000..8a3720af7 --- /dev/null +++ b/compose/update_plugins_and_tools.py @@ -0,0 +1,114 @@ +#!/usr/bin/env python3 + +import argparse +import io +import pathlib +import re +import shutil +from typing import Reversible, TextIO, List, Set, Mapping +import urllib3 +import zipfile + +import yaml + +def tool_key(tool: dict, revision: str = None) -> str: + if revision is None: + key = '-'.join([tool['name'], tool['owner'], tool['tool_shed_url']]) + else: + key = '-'.join([tool['name'], tool['owner'], tool['tool_shed_url'], revision]) + return key + +def load_extra_tools(tools_file: TextIO, known_tools: Set[str], tools: Mapping[str, dict]): + """load_extra_tools: + tools_file - Open file referring to a Galaxy tools.yaml format file with tools to add + known_tools - set of known tools - is modified in place + tools - list of tools - is modified in place + """ + data = yaml.load(tools_file, Loader=yaml.CLoader) + for tool in data['tools']: + for revision in tool['revisions']: + known_tools.add(tool_key(tool, revision)) + tools[tool_key(tool)] = tool + +def fetch_and_store_workflow(url: str, http: urllib3.PoolManager, + workflow_dir: str, known_tools: Set[str], tools: Mapping[str, dict]): + version_re = re.compile(r'.*(\d+\.\d+\.\d+).jar') + version_match = version_re.match(url) + if version_match is not None: + version_number = version_match.group(1) + else: + version_number = 'UNKNOWN' + + response = http.request('GET', url) + if response.status == 200: + workflow_filename = url.split('/')[-1] + print('fetching', workflow_filename) + open(workflow_dir + '/' + workflow_filename, 'wb').write(response.data) + content = zipfile.ZipFile(io.BytesIO(response.data)) + for path_string in content.namelist(): + if ('/' + version_number + '/tools.yaml') in path_string: + with content.open(path_string) as yaml_file: + data = yaml.load(yaml_file, Loader=yaml.CLoader) + for tool in data['tools']: + revisions_to_keep = [] + for revision in tool['revisions']: + key = tool_key(tool, revision) + if key not in known_tools: + revisions_to_keep.append(revision) + known_tools.add(key) + if len(revisions_to_keep) > 0: + tool['revisions'] = revisions_to_keep + this_tool_key = tool_key(tool) + if this_tool_key in tools: + tools[this_tool_key]['revisions'].extend(revisions_to_keep) + else: + tools[this_tool_key] = tool + + +if __name__ == '__main__': + parser = argparse.ArgumentParser(description='Set up environment for IRIDA and Galaxy deployment') + parser.add_argument('--remove_old_workflows', action='store_true', default=False, + help='Delete old workflows from the workflow dir') + parser.add_argument('--extra_tools_file', type=argparse.FileType(), + help='A Galaxy tools.yaml format file with tools to add in addition to the ones listed in the workflow jar files') + parser.add_argument('--workflow_dir', default='docker-svc/irida/workflows', help='Location to store downloaded workflow jar files') + parser.add_argument('--galaxy_tools_path', default='docker-svc/galaxy/galaxy-tools.yml', + help='File to store list of tools to install on Galaxy server') + parser.add_argument('workflow_file', type=argparse.FileType(), + help='File listing workflow URLs, one per line') + args = parser.parse_args() + + + workflow_output_path = pathlib.Path(args.workflow_dir) + if workflow_output_path.exists(): + if not workflow_output_path.is_dir(): + exit(f"Workflow output path ({workflow_output_path}) exists but it is not a directory") + elif args.remove_old_workflows: + shutil.rmtree(args.workflow_dir) + workflow_output_path.mkdir() + elif not workflow_output_path.exists(): + workflow_output_path.mkdir() + + known_tools = set() + tools = {} + if args.extra_tools_file is not None: + load_extra_tools(args.extra_tools_file, known_tools, tools) + + workflow_urls = [] + for line in args.workflow_file: + line = line.strip() + if line != '' and not line.startswith('#'): + workflow_urls.append(line.strip()) + + http = urllib3.PoolManager() + for url in workflow_urls: + fetch_and_store_workflow(url, http, args.workflow_dir, known_tools, tools) + + header = {'install_tool_dependencies': True, 'install_repository_dependencies': True, 'install_resolver_dependencies': True} + + tool_config = header + tool_list = [] + for key in tools: + tool_list.append(tools[key]) + tool_config['tools'] = tool_list + yaml.dump(tool_config, open(args.galaxy_tools_path, 'w'), Dumper=yaml.CDumper) diff --git a/compose/workflows.txt b/compose/workflows.txt new file mode 100644 index 000000000..6ab9cfbf3 --- /dev/null +++ b/compose/workflows.txt @@ -0,0 +1,2 @@ +https://github.com/COMBAT-SARS-COV-2/irida-plugin-sars-cov-2-illumina/releases/download/0.1.9/sarscov2-artic-illumina-pipeline-plugin-0.1.9.jar +https://github.com/COMBAT-SARS-COV-2/irida-plugin-sars-cov-2-nanopore/releases/download/0.1.3/sarscov2-artic-nanopore-pipeline-plugin-0.1.3.jar From 27e5611a3368fc6a2a278c3fdcb04df2e81ff276 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Thu, 18 Nov 2021 14:06:05 +0100 Subject: [PATCH 03/36] use newer Singularity release --- compose/base-images/galaxy-container-base/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/compose/base-images/galaxy-container-base/Dockerfile b/compose/base-images/galaxy-container-base/Dockerfile index 6cf33a516..1b4f52ee2 100644 --- a/compose/base-images/galaxy-container-base/Dockerfile +++ b/compose/base-images/galaxy-container-base/Dockerfile @@ -11,7 +11,7 @@ RUN apt update && apt install --no-install-recommends cryptsetup-bin uuid-dev -y && /usr/bin/common_cleanup.sh ENV PATH=/usr/local/go/bin:${PATH} -ENV SINGULARITY_VERSION=3.5.3 +ENV SINGULARITY_VERSION=3.7.3 RUN wget https://github.com/sylabs/singularity/releases/download/v${SINGULARITY_VERSION}/singularity-${SINGULARITY_VERSION}.tar.gz \ && tar -xzf singularity-${SINGULARITY_VERSION}.tar.gz \ && cd singularity \ From 045275bd161b25af0e600bf4c3b8d82659f0057c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Thu, 18 Nov 2021 14:26:19 +0100 Subject: [PATCH 04/36] try different link --- compose/base-images/galaxy-container-base/Dockerfile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/compose/base-images/galaxy-container-base/Dockerfile b/compose/base-images/galaxy-container-base/Dockerfile index 1b4f52ee2..eff744156 100644 --- a/compose/base-images/galaxy-container-base/Dockerfile +++ b/compose/base-images/galaxy-container-base/Dockerfile @@ -11,8 +11,8 @@ RUN apt update && apt install --no-install-recommends cryptsetup-bin uuid-dev -y && /usr/bin/common_cleanup.sh ENV PATH=/usr/local/go/bin:${PATH} -ENV SINGULARITY_VERSION=3.7.3 -RUN wget https://github.com/sylabs/singularity/releases/download/v${SINGULARITY_VERSION}/singularity-${SINGULARITY_VERSION}.tar.gz \ +ENV SINGULARITY_VERSION=3.5.3 +RUN wget https://github.com/singularityware/singularity/releases/download/v${SINGULARITY_VERSION}/singularity-${SINGULARITY_VERSION}.tar.gz \ && tar -xzf singularity-${SINGULARITY_VERSION}.tar.gz \ && cd singularity \ && ./mconfig \ From f126e0f0d9d19cb225e813ffb39baeb227c18e71 Mon Sep 17 00:00:00 2001 From: Peter van Heusden Date: Thu, 17 Mar 2022 09:13:11 +0200 Subject: [PATCH 05/36] Update IRIDA to version 22.04.1 --- compose/irida/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/compose/irida/Dockerfile b/compose/irida/Dockerfile index f42e80bfc..0a181d330 100644 --- a/compose/irida/Dockerfile +++ b/compose/irida/Dockerfile @@ -32,7 +32,7 @@ RUN set -ex; \ gosu nobody true; ENV IRIDA_DOWNLOAD_URL="https://github.com/phac-nml/irida/releases/download/" \ - IRIDA_VERSION="21.09" \ + IRIDA_VERSION="22.01.4" \ IRIDA_DATA_DIR=/data/irida \ JAVA_OPTS="-Dspring.profiles.active=prod -Dirida.db.profile=prod" \ GALAXY_ADMIN_USER="admin@galaxy.org" From adbdc03bf1f9d36e58c56fd323f62d059187ddda Mon Sep 17 00:00:00 2001 From: Peter van Heusden Date: Thu, 17 Mar 2022 09:13:41 +0200 Subject: [PATCH 06/36] Update login page to work with IRIDA 22 --- .../templates/irida/templates/login.html | 6 +++--- compose/irida/etc-irida/templates/login.html | 6 +++--- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/compose/galaxy-configurator/templates/irida/templates/login.html b/compose/galaxy-configurator/templates/irida/templates/login.html index e7ec4e600..09819af93 100644 --- a/compose/galaxy-configurator/templates/irida/templates/login.html +++ b/compose/galaxy-configurator/templates/irida/templates/login.html @@ -8,8 +8,8 @@ emailConfigured: /*[[${emailConfigured}]]*/ false }; - - + +