Fix bug: convert_targetp still has problems when installed in a virtualenv

psot/nextflow.py

@@ -19,6 +19,7 @@ analysis_template = Template ('''
 process ${id} {
     executor '${executor}'
     ${clusterOptions}
+    ${beforeScript}
     input:
     file fasta from for_${id}${chunks}
 
@@ -50,6 +51,7 @@ process generate_${id}_live_results {
 ''')
 convert_live_template = Template ('''
 process convert_${id}_to_json {
+    ${beforeScript}
     input:
     file result from ${id}_results
 
@@ -64,6 +66,7 @@ process convert_${id}_to_json {
 ''')
 convert_info_template = Template ('''
 process convert_${id}_to_json {
+    ${beforeScript}
     input:
     file result from ${id}_results
 
@@ -78,6 +81,7 @@ process convert_${id}_to_json {
 ''')
 convert_template = Template ('''
 process convert_${id}_to_json {
+    ${beforeScript}
     input:
     file result from ${id}_results
 
@@ -92,6 +96,7 @@ process convert_${id}_to_json {
 ''')
 retrieve_informations_template = Template('''
 process retrieve_informations_for_${id} {
+    ${beforeScript}
 
     input:
     file result from ${id}_json_info
@@ -107,6 +112,7 @@ process retrieve_informations_for_${id} {
 ''')
 retrieve_informations_live_template = Template('''
 process retrieve_informations_for_${id} {
+    ${beforeScript}
 
     input:
     file result from ${id}_json_info
@@ -187,12 +193,16 @@ Channel.fromPath(params.fasta).set{fasta}''')
 
     for m in modules:
         config = flatten(m)
+        config['output'] = execution['output']
+        if 'venv' in execution:
+            config['beforeScript'] = "beforeScript 'export PS1=; source " + execution['venv'] + "/bin/activate'"
+        else:
+            config['beforeScript'] = ''
+
         if execution['use_cluster']:
             config['executor'] = 'sge'
             config['chunks'] = ".splitFasta(by:300, file:'input')"
             config['clusterOptions'] = "clusterOptions='-S /bin/bash'"
-            if 'venv' in execution:
-              config['clusterOptions'] = config['clusterOptions'] + "\nbeforeScript 'export PS1=; source " + execution['venv'] + "/bin/activate'"
         else:
             config['executor'] = 'local'
             config['chunks'] = ''
@@ -200,21 +210,17 @@ Channel.fromPath(params.fasta).set{fasta}''')
 
         fragments.append(analysis_template.substitute(config))
         if execution['mode'] == 'live' and not execution['fetch_informations']:
-            fragments.append(convert_live_template.substitute(flatten(m)))
-            copy = deepcopy(m)
-            copy['output'] = execution['output']
-            fragments.append(live_results_template.substitute(flatten(copy)))
+            fragments.append(convert_live_template.substitute(config))
+            fragments.append(live_results_template.substitute(config))
         elif execution['mode'] == 'live' and execution['fetch_informations']:
-            fragments.append(convert_info_template.substitute(flatten(m)))
-            fragments.append(retrieve_informations_live_template.substitute(flatten(m)))
-            copy = deepcopy(m)
-            copy['output'] = execution['output']
-            fragments.append(live_results_template.substitute(flatten(copy)))
+            fragments.append(convert_info_template.substitute(config))
+            fragments.append(retrieve_informations_live_template.substitute(config))
+            fragments.append(live_results_template.substitute(config))
         elif execution['mode'] == 'complete' and execution['fetch_informations']:
-          fragments.append(convert_info_template.substitute(flatten(m)))
-          fragments.append(retrieve_informations_template.substitute(flatten(m)))
+          fragments.append(convert_info_template.substitute(config))
+          fragments.append(retrieve_informations_template.substitute(config))
         else:
-            fragments.append(convert_template.substitute(flatten(m)))
+            fragments.append(convert_template.substitute(config))
 
     json_inputs = []
     for m in modules:

psot/scripts/convert_targetp.py

-#!/usr/bin/python3
+#!/usr/bin/env python3
 
 import sys
 import json