Merge pull request #156 from cancervariants/staging

Staging

.ebextensions/02_download_variant_data_commands.config → .ebextensions/02_app_config.config

@@ -1,50 +1,50 @@
-container_commands:
-    01_export_eb_env_var:
-        command: "export $(cat /opt/elasticbeanstalk/deployment/env | xargs)"
-
-    02_install_awscli:
+commands:
+    01_install_postgresql_devel:
+        command: "yum install -y python-devel postgresql-devel"
+    02_install_aws_cli:
         command: "yum install -y awscli"
-
     03_install_unzip:
-        test: test ! -d "/usr/local/share/seqrepo"
         command: "yum install -y unzip"
+    04_export_eb_env_var:
+        command: "export $(cat /opt/elasticbeanstalk/deployment/env | xargs)"
 
-    05_refseq_gene_symbols_download:
+container_commands:
+    01_refseq_gene_symbols_download:
         test: test ! -f "/var/app/venv/staging-LQM1lest/lib/python3.8/site-packages/variation/data/refseq_gene_symbols.txt"
         command: "aws s3 cp s3://${AWS_BUCKET_NAME}/variation/refseq_gene_symbols.txt /var/app/venv/staging-LQM1lest/lib/python3.8/site-packages/variation/data/refseq_gene_symbols.txt --region us-east-2"
 
-    06_mane_grch38_refseq_download:
+    02_mane_grch38_refseq_download:
         test: test ! -f "/var/app/venv/staging-LQM1lest/lib/python3.8/site-packages/variation/data/MANE.GRCh38.v0.93.summary.txt"
         command: "aws s3 cp s3://${AWS_BUCKET_NAME}/variation/MANE.GRCh38.v0.93.summary.txt /var/app/venv/staging-LQM1lest/lib/python3.8/site-packages/variation/data/MANE.GRCh38.v0.93.summary.txt --region us-east-2"
 
-    07_s3_download:
+    03_s3_download:
         test: test ! -d "/usr/local/share/seqrepo"
         command: "aws s3 cp s3://${AWS_BUCKET_NAME}/${AWS_SEQREPO_OBJECT} /usr/local/share/seqrepo.zip --region us-east-2"
 
-    08_unzip_seqrepo:
+    04_unzip_seqrepo:
         test: test -f "/usr/local/share/seqrepo.zip"
         command: "unzip /usr/local/share/seqrepo.zip -d /usr/local/share"
 
-    09_seqrepo_permission:
+    05_seqrepo_permission:
         test: test -d "/usr/local/share/seqrepo"
         command: "chmod -R 777 /usr/local/share/seqrepo"
 
-    10_macosx_permission:
+    06_macosx_permission:
         test: test -d "/usr/local/share/__MACOSX"
         command: "chmod -R +wr /usr/local/share/__MACOSX"
 
-    11_seqrepo_zip_permission:
+    07_seqrepo_zip_permission:
         test: test -f "/usr/local/share/seqrepo.zip"
         command: "chmod +wr /usr/local/share/seqrepo.zip"
 
-    12_remove_macosx:
+    08_remove_macosx:
         test: test -d "/usr/local/share/__MACOSX"
         command: "rm -R /usr/local/share/__MACOSX"
 
-    13_remove_seqrepo_zip:
+    09_remove_seqrepo_zip:
         test: test -f "/usr/local/share/seqrepo.zip"
         command: "rm /usr/local/share/seqrepo.zip"
 
-    14_data_permission:
+    10_data_permission:
         test: test -d "/usr/local/share/seqrepo"
         command: "chmod -R +wrx /usr/local/share/seqrepo"