Issue 26 - changes for remote execution (#28)

* - Pipeline adjustments for new (remote) cell executor
  (where params are placed in a config file)
- Adds pull policy to sdposter (default is Always)
- Adds 'retry' to gitignore

* - Use of literal | in nextflow configs

* - publishDir is now $baseDir/results (mode symlink)

* - Ansible now display tag of poster image

* - Experiment with 'copy' mode

* - Now using move for results

* - Removed docker config

* - Removed content from nextflow config files

Author: alanbchristie

.gitignore

@@ -12,4 +12,5 @@ work
 .nextflow.log*
 /tmp
 **/*.egg-info
-**/.DS_Store
+**/.DS_Store
+*.retry

openshift/ansible/ansible.cfg

@@ -1,2 +1,4 @@
 [defaults]
+callback_whitelist = profile_tasks
 inventory = inventory
+nocows = 1

openshift/ansible/roles/pipelines/files/post-service-descriptors.yaml

@@ -21,6 +21,8 @@ parameters:
   value: latest
 - name: POSTER_SA
   value: squonk
+- name: PULL_POLICY
+  value: Always
 
 objects:
 
@@ -42,5 +44,6 @@ objects:
         containers:
         - image: squonk/rdkit-pipelines-sdposter:${POSTER_IMAGE_TAG}
           name: pipelines-sd-poster
+          imagePullPolicy: ${PULL_POLICY}
 
         restartPolicy: Never

openshift/ansible/roles/pipelines/tasks/main.yaml

@@ -21,7 +21,7 @@
   shell: oc delete jobs/{{ job_name }}
   when: jobs_result.stdout | regex_search('^%s' % job_name, multiline=True)
 
-- name: Run SD poster job (always)
+- name: Run SD poster job (always) (tag={{ oc_pipelines_sd_poster_image_tag }})
   shell: >
     oc process
     -f {{ role_path }}/files/post-service-descriptors.yaml

src/nextflow/docking/plip.config

@@ -1,4 +1 @@
-docker.enabled = true
-docker.mountFlags = 'z'
-docker.runOptions = '-u $(id -u):$(id -g)'
-process.container = 'informaticsmatters/pli:latest'
+// Intentionally Empty

src/nextflow/docking/plip.nsd.config

@@ -1,3 +1 @@
-docker.enabled = true
-docker.mountFlags = 'z'
-process.container = 'informaticsmatters/pli:latest'
+// Intentionally Empty

src/nextflow/docking/plip.nsd.nf

@@ -51,7 +51,7 @@ process joiner {
 
     container 'informaticsmatters/pli:latest'
     beforeScript 'chmod g+w .'
-    publishDir baseDir, mode: 'link'
+    publishDir "$baseDir/results", mode: 'move'
 
     input:
     file parts from scored_parts.collect()

src/nextflow/docking/plip.nsd.yml

@@ -49,4 +49,5 @@ inputRoutes:
 - route: "FILE"
 outputRoutes:
 - route: "FILE"
-nextflowParams: "${binding.variables.containsKey('score') ? ' --score ' + score: ''}"
+nextflowParams: |
+  ${binding.variables.containsKey('score') ? 'params.score = ' + score : ''}

src/nextflow/docking/rdock.config

@@ -1,7 +1 @@
-docker.enabled = true
-// allow to run with SELinux
-docker.mountFlags = 'z'
-// this runs the containers as the current user
-docker.runOptions = '-u $(id -u):$(id -g)'
-// See here for information on this image: https://github.com/InformaticsMatters/rdock_docker
-process.container = 'informaticsmatters/rdock-mini:latest'
+// Intentionally Empty

src/nextflow/docking/rdock.nsd.config

@@ -1,3 +1 @@
-docker.enabled = true
-docker.mountFlags = 'z'
-process.container = 'informaticsmatters/rdkit_pipelines'
+// Intentionally Empty