Merge remote-tracking branch 'upstream/master' into arteria-staging

Conflicts: README.md
NationalGenomicsInfrastructure · Sep 20, 2016 · 4bdea70 · 4bdea70
2 parents afc30f5 + fe9ad4b
commit 4bdea70
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diff --git a/README.md b/README.md
@@ -100,6 +100,9 @@ And then inside a screen on irma1 start two windows with the corresponding comma
 /lupus/ngi/staging/latest/sw/arteria/siswrap_venv/staging/bin/siswrap-ws --configroot=/lupus/ngi/staging/latest/conf/arteria/siswrap/staging/ --port=10431 --debug
 /lupus/ngi/staging/latest/sw/arteria/siswrap_venv/staging/bin/siswrap-ws --configroot=/lupus/ngi/staging/latest/conf/arteria/siswrap/staging/ --port=10431 --debug
 ```
+####Nota bene
+
+Remember that you will probably have to restart services manually after a new production release have been rolled out. First re-load the crontab as the func user on irma1 with a `crontab /lupus/ngi/production/latest/conf/crontab_SITE`. Then, depending on what software your func user is running, continue with manually shutting down the old versions and re-start the new versions of the software. 
 
 ###Manual initiations on irma1
 

diff --git a/roles/ngi_pipeline/templates/create_ngi_pipeline_dirs.sh.j2 b/roles/ngi_pipeline/templates/create_ngi_pipeline_dirs.sh.j2
@@ -19,7 +19,7 @@ mkdir -p {{ proj_root }}/$1/private/log
 mkdir -p {{ proj_root }}/$1/private/db
 mkdir -p {{ proj_root }}/$1/nobackup/NGI/softlinks
 mkdir -p {{ proj_root }}/$1/private/log/supervisord
-ln -s {{ ngi_pipeline_dest }}/DELIVERY.README.txt {{ proj_root }}/$1/nobackup/NGI/softlinks/DELIVERY.README.txt
-ln -s {{ ngi_pipeline_dest }}/scripts/applyRecalibration.sh {{ proj_root }}/$1/nobackup/NGI/softlinks/applyRecalibration.sh
-ln -s {{ ngi_pipeline_dest }}/scripts/bam2fastq.sh {{ proj_root }}/$1/nobackup/NGI/softlinks/bam2fastq.sh
+ln -s /lupus/ngi/production/latest/sw/ngi_pipeline/DELIVERY.README.txt {{ proj_root }}/$1/nobackup/NGI/softlinks/DELIVERY.README.txt
+ln -s /lupus/ngi/production/latest/sw/ngi_pipeline/scripts/applyRecalibration.sh {{ proj_root }}/$1/nobackup/NGI/softlinks/applyRecalibration.sh
+ln -s /lupus/ngi/production/latest/sw/ngi_pipeline/scripts/bam2fastq.sh {{ proj_root }}/$1/nobackup/NGI/softlinks/bam2fastq.sh
 
diff --git a/roles/ngi_pipeline/templates/sourceme_common.sh.j2 b/roles/ngi_pipeline/templates/sourceme_common.sh.j2
@@ -11,5 +11,13 @@ export LANG=en_US.UTF-8
 
 # Append the Bash prompt with the version of the Irma environment/provisioning
 # that we're running. 
-IRMA_ENV=`echo $BASH_SOURCE | cut -d/ -f4,5`
-export PS1="(irma env: $IRMA_ENV) $PS1"
+IRMA_ENV=`echo $BASH_SOURCE | cut -d/ -f4`
+IRMA_VER=`echo $BASH_SOURCE | cut -d/ -f5`
+
+if [ $IRMA_ENV == "production" ] ; then
+	IRMA_PROMPT="Prod/$IRMA_VER"
+else
+	IRMA_PROMPT="Stage/$IRMA_VER"
+fi
+
+export PS1="$IRMA_PROMPT $PS1"
diff --git a/tasks/pre-install.yml b/tasks/pre-install.yml
@@ -66,6 +66,9 @@
   - name: set proj root for production
     set_fact: 
       proj_root: "/proj/"
+  - name: set delivery root for production
+    set_fact: 
+      milou_delivery_root: "/pica/sw/links/proj/"
     when: deployment_environment == "production"
 
   # charon variables are fetched from private host_vars/127.0.0.1/charon_credentials.yml