From 693ec0f5bbc6deb525d01f2f7a68376d51648632 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= <bjoern@gruenings.eu>
Date: Wed, 31 May 2017 23:13:20 +0200
Subject: [PATCH 01/18] update to version 17.05

---
 Dockerfile | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 3d85da2..e80c702 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,8 +1,6 @@
 # Galaxy - GalaxyP
-#
-# VERSION       0.1
 
-FROM quay.io/bgruening/galaxy:17.01
+FROM bgruening/galaxy-stable:17.05
 
 MAINTAINER Björn A. Grüning, bjoern.gruening@gmail.com
 

From 3a8591a75938ba740cc51b2c7fc196b6bff59e37 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= <bjoern@gruenings.eu>
Date: Wed, 31 May 2017 23:14:08 +0200
Subject: [PATCH 02/18] Update galaxyp_wf.yaml

---
 galaxyp_wf.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/galaxyp_wf.yaml b/galaxyp_wf.yaml
index 06b3a9a..a632e42 100644
--- a/galaxyp_wf.yaml
+++ b/galaxyp_wf.yaml
@@ -38,11 +38,11 @@
 
 api_key: admin
 galaxy_instance: http://localhost:8080
+install_resolver_dependencies: true
+install_tool_dependencies: false
 tools:
 - name: asms_tutorial_2016
   owner: galaxyp
   tool_panel_section_label: "ASMS 2016"
-  tool_shed_url: https://toolshed.g2.bx.psu.edu
-
 
 

From 874b6ac0c294a2ce8232acffd50cae0d1ae53b3b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= <bjoern@gruenings.eu>
Date: Wed, 31 May 2017 23:25:03 +0200
Subject: [PATCH 03/18] Update .travis.yml

---
 .travis.yml | 27 +++++++++++----------------
 1 file changed, 11 insertions(+), 16 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index bab434d..b85c986 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -13,22 +13,17 @@ git:
   submodules: false
 
 before_install:
-  - export GALAXY_TRAVIS_USER=galaxy
-  - export GALAXY_UID=1450
-  - export GALAXY_GID=1450
-  - export GALAXY_HOME=/home/galaxy
-  - export GALAXY_USER=admin@galaxy.org
-  - export GALAXY_USER_EMAIL=admin@galaxy.org
-  - export GALAXY_USER_PASSWD=admin
-  - export BIOBLEND_GALAXY_API_KEY=admin
-  - export BIOBLEND_GALAXY_URL=http://localhost:8080
+  - wget https://raw.githubusercontent.com/bgruening/galaxy-flavor-testing/master/Makefile
+  - make docker_install
+  - travis_wait 45 make docker_build
+  - make docker_run
+  - sleep 300
 
-  - sudo apt-get update -qq
-  - sudo apt-get install docker-engine --no-install-recommends -y -o Dpkg::Options::="--force-confmiss" -o Dpkg::Options::="--force-confdef" -o Dpkg::Options::="--force-confnew"
-
-  - docker --version
-  - docker info
+install:
+  - make install
 
 script:
-  - travis_wait 45 docker build -t galaxy-docker/test .
-
+  - make test_api
+  - make test_ftp
+  - make test_bioblend
+  #- make test_docker_in_docker

From 88c36dc00f59f268e6e36b576206d19f45ba1dcf Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= <bjoern@gruenings.eu>
Date: Thu, 1 Jun 2017 18:00:09 +0200
Subject: [PATCH 04/18] Update .travis.yml

---
 .travis.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index b85c986..804896c 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -15,7 +15,7 @@ git:
 before_install:
   - wget https://raw.githubusercontent.com/bgruening/galaxy-flavor-testing/master/Makefile
   - make docker_install
-  - travis_wait 45 make docker_build
+  - make docker_build
   - make docker_run
   - sleep 300
 

From 1cb62e70570ca15991a026162fdf9c78930cc4f0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= <bjoern@gruenings.eu>
Date: Thu, 1 Jun 2017 18:46:52 +0200
Subject: [PATCH 05/18] Update .travis.yml

---
 .travis.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index 804896c..be0a392 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -20,7 +20,7 @@ before_install:
   - sleep 300
 
 install:
-  - make install
+  - travis_wait 75 make install
 
 script:
   - make test_api

From 29df9e9f5541088c9e29b751fba3c826bc2e92b9 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= <bjoern@gruenings.eu>
Date: Thu, 1 Jun 2017 19:30:14 +0200
Subject: [PATCH 06/18] Update .travis.yml

---
 .travis.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index be0a392..b73fe4b 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -15,12 +15,12 @@ git:
 before_install:
   - wget https://raw.githubusercontent.com/bgruening/galaxy-flavor-testing/master/Makefile
   - make docker_install
-  - make docker_build
+  - travis_wait 75 make docker_build
   - make docker_run
   - sleep 300
 
 install:
-  - travis_wait 75 make install
+  - make install
 
 script:
   - make test_api

From 43a093e2dcca301cfd1a762128c35aa1e7b2184c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= <bjoern@gruenings.eu>
Date: Thu, 1 Jun 2017 20:31:24 +0200
Subject: [PATCH 07/18] Update galaxyp.yaml

---
 galaxyp.yaml | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/galaxyp.yaml b/galaxyp.yaml
index 48bd6e8..9ce6e48 100644
--- a/galaxyp.yaml
+++ b/galaxyp.yaml
@@ -211,10 +211,6 @@ tools:
   owner: galaxyp
   tool_panel_section_id: utils
 
-- name: openms
-  owner: galaxyp
-  tool_panel_section_label: OpenMS
-
 - name: spectrast
   owner: iracooke
   tool_panel_section_label: SpectraST

From 83c59bcc7f0f6c36a6bee48653bea60f11499f0c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= <bjoern@gruenings.eu>
Date: Thu, 1 Jun 2017 21:29:40 +0200
Subject: [PATCH 08/18] Update galaxyp.yaml

---
 galaxyp.yaml | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/galaxyp.yaml b/galaxyp.yaml
index 9ce6e48..bc2d537 100644
--- a/galaxyp.yaml
+++ b/galaxyp.yaml
@@ -211,10 +211,6 @@ tools:
   owner: galaxyp
   tool_panel_section_id: utils
 
-- name: spectrast
-  owner: iracooke
-  tool_panel_section_label: SpectraST
-
 - name: feature_alignment
   owner: galaxyp
   tool_panel_section_label: SpectraST

From fd6faae54ee43da494ab79ee2ab7ebf7ad929487 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= <bjoern@gruenings.eu>
Date: Thu, 1 Jun 2017 22:18:14 +0200
Subject: [PATCH 09/18] Update galaxyp.yaml

---
 galaxyp.yaml | 18 ------------------
 1 file changed, 18 deletions(-)

diff --git a/galaxyp.yaml b/galaxyp.yaml
index bc2d537..f3b8ddc 100644
--- a/galaxyp.yaml
+++ b/galaxyp.yaml
@@ -141,24 +141,6 @@ tools:
   owner: galaxyp
   tool_panel_section_label: "Post Translational Modifications"
 
-- name: package_directag
-  owner: galaxyp
-
-- name: package_myrimatch
-  owner: galaxyp
-
-- name: package_mgf_formatter
-  owner: galaxyp
-
-- name: package_ltq_iquant_cli
-  owner: galaxyp
-
-- name: package_idpqonvert
-  owner: galaxyp
-
-- name: package_tagrecon
-  owner: galaxyp
-
 - name: directag_and_tagrecon
   owner: galaxyp
   tool_panel_section_label: Bumbershoot

From 1020c9829352d720529fa3fadcf1ca2c035d10c3 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= <bjoern@gruenings.eu>
Date: Thu, 1 Jun 2017 23:06:10 +0200
Subject: [PATCH 10/18] Update galaxyp.yaml

---
 galaxyp.yaml | 62 ----------------------------------------------------
 1 file changed, 62 deletions(-)

diff --git a/galaxyp.yaml b/galaxyp.yaml
index f3b8ddc..27586ae 100644
--- a/galaxyp.yaml
+++ b/galaxyp.yaml
@@ -41,54 +41,6 @@ galaxy_instance: http://localhost:8080
 install_resolver_dependencies: true
 install_tool_dependencies: false
 tools:
-- name: fasta_compute_length
-  owner: devteam
-  tool_panel_section_label: "FASTA Tools"
-
-- name: fasta_merge_files_and_filter_unique_sequences
-  owner: galaxyp
-  tool_panel_section_label: "FASTA Tools"
-
-- name: seq_filter_by_id
-  owner: peterjc
-  tool_panel_section_label: "FASTA Tools"
-
-- name: seq_rename
-  owner: peterjc
-  tool_panel_section_label: "FASTA Tools"
-
-- name: seq_select_by_id
-  owner: peterjc
-  tool_panel_section_label: "FASTA Tools"
-
-- name: fasta_formatter
-  owner: devteam
-  tool_panel_section_label: "FASTA Tools"
-
-- name: fasta_nucleotide_changer
-  owner: devteam
-  tool_panel_section_label: "FASTA Tools"
-
-- name: fasta_to_tabular
-  owner: devteam
-  tool_panel_section_label: "FASTA Tools"
-
-- name: find_subsequences
-  owner: bgruening
-  tool_panel_section_label: "FASTA Tools"
-
-- name: tabular_to_fasta
-  owner: devteam
-  tool_panel_section_label: "FASTA Tools"
-
-- name: fasta_filter_by_length
-  owner: devteam
-  tool_panel_section_label: "FASTA Tools"
-
-- name: decoyfasta
-  owner: galaxyp
-  tool_panel_section_label: "FASTA Tools"
-
 - name: text_processing
   owner: bgruening
   tool_panel_section_id: "textutil"
@@ -193,20 +145,6 @@ tools:
   owner: galaxyp
   tool_panel_section_id: utils
 
-- name: feature_alignment
-  owner: galaxyp
-  tool_panel_section_label: SpectraST
-
-- name: spectrast2spectrast_irt
-  owner: galaxyp
-  tool_panel_section_label: SpectraST
-  tool_shed_url: http://testtoolshed.g2.bx.psu.edu/
-
-- name: spectrast2tsv
-  owner: galaxyp
-  tool_panel_section_label: SpectraST
-  tool_shed_url: http://testtoolshed.g2.bx.psu.edu/
-
 - name: percolator
   owner: galaxyp
   tool_panel_section_label: Percolator

From 8b96e2e591750e41db620bd46ca22547b589af95 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= <bjoern@gruenings.eu>
Date: Thu, 1 Jun 2017 23:51:05 +0200
Subject: [PATCH 11/18] Update Dockerfile

---
 Dockerfile | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index e80c702..91e8df4 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -11,8 +11,8 @@ ADD galaxyp.yaml $GALAXY_ROOT/tools.yaml
 ADD galaxyp_wf.yaml $GALAXY_ROOT/workflows.yaml
 
 RUN install-tools $GALAXY_ROOT/workflows.yaml && \
-    install-tools $GALAXY_ROOT/tools.yaml
-
+    install-tools $GALAXY_ROOT/tools.yaml && \
+    /tool_deps/_conda/bin/conda clean --tarballs
 # Data libraries
 ADD library_data.yaml $GALAXY_ROOT/library_data.yaml
 

From 1700eb4e635b5be5c6ecb258d960afd3b76e258e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= <bjoern@gruenings.eu>
Date: Fri, 2 Jun 2017 00:37:53 +0200
Subject: [PATCH 12/18] Update galaxyp.yaml

---
 galaxyp.yaml | 8 --------
 1 file changed, 8 deletions(-)

diff --git a/galaxyp.yaml b/galaxyp.yaml
index 27586ae..bd954dd 100644
--- a/galaxyp.yaml
+++ b/galaxyp.yaml
@@ -49,14 +49,6 @@ tools:
   owner: devteam
   tool_panel_section_id: "textutil"
 
-- name: regex_find_replace
-  owner: jjohnson
-  tool_panel_section_id: "textutil"
-
-- name: bedtools
-  owner: iuc
-  tool_panel_section_label: "BED Tools"
-
 - name: translate_bed_sequences
   owner: jjohnson
   tool_panel_section_label: "BED Tools"

From 55222bab7d37a450356d2c922f67ee19b5c5aa48 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= <bjoern@gruenings.eu>
Date: Fri, 2 Jun 2017 00:39:48 +0200
Subject: [PATCH 13/18] Update Dockerfile

---
 Dockerfile | 13 +------------
 1 file changed, 1 insertion(+), 12 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 91e8df4..a8f4df5 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -8,17 +8,6 @@ ENV GALAXY_CONFIG_BRAND Galaxy for Proteomic Research
 
 # Install tools
 ADD galaxyp.yaml $GALAXY_ROOT/tools.yaml
-ADD galaxyp_wf.yaml $GALAXY_ROOT/workflows.yaml
 
-RUN install-tools $GALAXY_ROOT/workflows.yaml && \
-    install-tools $GALAXY_ROOT/tools.yaml && \
+RUN install-tools $GALAXY_ROOT/tools.yaml && \
     /tool_deps/_conda/bin/conda clean --tarballs
-# Data libraries
-ADD library_data.yaml $GALAXY_ROOT/library_data.yaml
-
-# Download training data and populate the data library
-RUN startup_lite && \
-    sleep 60 && \
-    . $GALAXY_VIRTUAL_ENV/bin/activate && \
-    python /usr/local/lib/python2.7/dist-packages/ephemeris/setup_data_libraries.py -i $GALAXY_ROOT/library_data.yaml && \
-    workflow-install --workflow_path $GALAXY_HOME/workflows/ -g http://localhost:8080 -u $GALAXY_DEFAULT_ADMIN_USER -p $GALAXY_DEFAULT_ADMIN_PASSWORD

From 8e3daa1d492dc065441abc5bd370a7aab7a55bb3 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= <bjoern@gruenings.eu>
Date: Fri, 2 Jun 2017 05:54:00 +0200
Subject: [PATCH 14/18] Update Dockerfile

---
 Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Dockerfile b/Dockerfile
index a8f4df5..fac4ce6 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,6 +1,6 @@
 # Galaxy - GalaxyP
 
-FROM bgruening/galaxy-stable:17.05
+FROM bgruening/galaxy-sequence-tools:17.05
 
 MAINTAINER Björn A. Grüning, bjoern.gruening@gmail.com
 

From 95b566b5739cc5ef9923beb3e075ab60d1f893ad Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= <bjoern@gruenings.eu>
Date: Fri, 2 Jun 2017 05:54:26 +0200
Subject: [PATCH 15/18] Delete library_data.yaml

---
 library_data.yaml | 10 ----------
 1 file changed, 10 deletions(-)
 delete mode 100644 library_data.yaml

diff --git a/library_data.yaml b/library_data.yaml
deleted file mode 100644
index 1e897a2..0000000
--- a/library_data.yaml
+++ /dev/null
@@ -1,10 +0,0 @@
-libraries:
-    - name: test1
-      files:
-        - https://raw.githubusercontent.com/bgruening/galaxytools/master/tools/augustus/test-data/human_augustus.fa
-        - https://raw.githubusercontent.com/bgruening/galaxytools/master/tools/augustus/test-data/human_augustus.fa
-    - name: test2
-      files:
-        - https://raw.githubusercontent.com/bgruening/galaxytools/master/tools/augustus/test-data/human_augustus_utr-on.gtf
-        - https://raw.githubusercontent.com/bgruening/galaxytools/master/tools/augustus/test-data/human_augustus_utr-on.gtf
-        - https://raw.githubusercontent.com/bgruening/galaxytools/master/tools/augustus/test-data/human_augustus_utr-on.gtf

From 0c34c1444524813f63015ff867d0d51d2bcac319 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= <bjoern@gruenings.eu>
Date: Fri, 2 Jun 2017 05:54:59 +0200
Subject: [PATCH 16/18] Delete galaxyp_wf.yaml

---
 galaxyp_wf.yaml | 48 ------------------------------------------------
 1 file changed, 48 deletions(-)
 delete mode 100644 galaxyp_wf.yaml

diff --git a/galaxyp_wf.yaml b/galaxyp_wf.yaml
deleted file mode 100644
index a632e42..0000000
--- a/galaxyp_wf.yaml
+++ /dev/null
@@ -1,48 +0,0 @@
----
-# This is a sample file to be used as a reference for populating a list of
-# tools that you wish to install into Galaxy from a Tool Shed via the
-# `install_tool_shed_tools.py` script.
-#
-# For each tool you want to install, you must provide the following keys:
-#  * name: this is is the name of the tool to install
-#  * owner: owner of the Tool Shed repository from where the tools is being
-#           installed
-# Further, you need to provide **one** of the following two keys:
-#  * tool_panel_section_id: ID of the tool panel section where you want the
-#                           tool to be installed. The section ID can be found
-#                           in Galaxy's `shed_tool_conf.xml` config file. Note
-#                           that the specified section must exist in this file.
-#                           Otherwise, the tool will be installed outside any
-#                           section.
-#  * tool_panel_section_label: Display label of a tool panel section where
-#                              you want the tool to be installed. If it does not
-#                              exist, this section will be created on the target
-#                              Galaxy instance (note that this is different than
-#                              when using the ID).
-#                              Multi-word labels need to be placed in quotes.
-#                              Each label will have a corresponding ID created;
-#                              the ID will be an all lowercase version of the
-#                              label, with multiple words joined with
-#                              underscores (e.g., 'BED tools' -> 'bed_tools').
-#
-# You can also specify the following optional keys to further define the
-# installation properties:
-#  * tool_shed_url: the URL of the Tool Shed from where the tool should be
-#                   installed. (default: https://toolshed.g2.bx.psu.edu)
-#  * revisions: a list of revisions of the tool, all of which will attempt to
-#               be installed. (default: latest)
-#  * install_tool_dependencies: True or False - whether to install tool
-#                               dependencies or not. (default: True)
-#  * install_repository_dependencies: True or False - whether to install repo
-#                               dependencies or not. (default: True)
-
-api_key: admin
-galaxy_instance: http://localhost:8080
-install_resolver_dependencies: true
-install_tool_dependencies: false
-tools:
-- name: asms_tutorial_2016
-  owner: galaxyp
-  tool_panel_section_label: "ASMS 2016"
-
-

From 7316c1ccfcab6355ab3c921b8473e5e532500eb7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= <bjoern@gruenings.eu>
Date: Sun, 4 Jun 2017 17:39:07 +0200
Subject: [PATCH 17/18] Update galaxyp.yaml

---
 galaxyp.yaml | 16 ----------------
 1 file changed, 16 deletions(-)

diff --git a/galaxyp.yaml b/galaxyp.yaml
index bd954dd..ce84f91 100644
--- a/galaxyp.yaml
+++ b/galaxyp.yaml
@@ -81,10 +81,6 @@ tools:
   owner: galaxyp
   tool_panel_section_id: convert
 
-- name: morpheus
-  owner: galaxyp
-  tool_panel_section_label: "Post Translational Modifications"
-
 - name: directag_and_tagrecon
   owner: galaxyp
   tool_panel_section_label: Bumbershoot
@@ -109,14 +105,6 @@ tools:
   owner: galaxyp
   tool_panel_section_id: utils
 
-- name: ms_wiff_loader
-  owner: galaxyp
-  tool_panel_section_id: utils
-
-- name: myrimatch
-  owner: galaxyp
-  tool_panel_section_label: Bumbershoot
-
 - name: peptide_to_gff
   owner: galaxyp
   tool_panel_section_id: utils
@@ -125,10 +113,6 @@ tools:
   owner: galaxyp
   tool_panel_section_id: utils
 
-- name: proteinpilot
-  owner: galaxyp
-  tool_panel_section_id: utils
-
 - name: protxml_to_xls
   owner: galaxyp
   tool_panel_section_id: utils

From b83a7fac9a9f01126d0af6649b4d9126d2f1afc7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= <bjoern@gruenings.eu>
Date: Sun, 4 Jun 2017 18:39:50 +0200
Subject: [PATCH 18/18] Update galaxyp.yaml

---
 galaxyp.yaml | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/galaxyp.yaml b/galaxyp.yaml
index ce84f91..e90fa2a 100644
--- a/galaxyp.yaml
+++ b/galaxyp.yaml
@@ -73,10 +73,6 @@ tools:
   owner: galaxyp
   tool_panel_section_label: "BLAST"
 
-- name: blast_plus_remote_blastp
-  owner: galaxyp
-  tool_panel_section_label: "BLAST"
-
 - name: mgf_formatter
   owner: galaxyp
   tool_panel_section_id: convert