add "docker" and "singularity" programm arguments to psot; extend scripts and...

add "docker" and "singularity" programm arguments to psot; extend scripts and config files for blastp, ghostx and hmmer

psot/default_repo/modules/blast_vs_swissprot.yaml

@@ -14,6 +14,7 @@ analysis:
         database: '/vol/biodb/uniprot/uniprot_sprot.fasta'
         evalue: 1e-10
         use_accession:
+    container: 'blastp_swissprot'
 
 # The name of the result to json converter script. Must take one parameter, the
 # result file from the analysis_script

psot/default_repo/modules/ghostx_vs_swissprot.yaml

@@ -12,6 +12,7 @@ analysis:
     script: 'run_ghostx.py'
     parameters:
         database: '/vol/biodb/ghostx/uniprot_sprot'
+    container: 'ghostx_swissprot'
 
 # The name of the result to json converter script. Must take one parameter, the
 # result file from the analysis_script

psot/default_repo/modules/hmmer_vs_PFAM-A.yaml

@@ -16,6 +16,7 @@ analysis:
     execution:
         cluster:
             chunksize: 200
+    container: 'hmmer_pfam_a'
 
 # The name of the result to json converter script. Must take one parameter, the
 # result file from the analysis_script

psot/default_repo/profiles/custom.yaml

+name: 'custom'
+info: 'Profile that contains tools for testing and development'
+modules:
+  signalp:
+      organism: 'euk'

psot/default_repo/profiles/custom2.yaml

+name: 'custom2'
+info: 'Profile that contains tools for more testing'
+modules:
+  targetp:
+      organism_group: 'non-plant'
+  signalp:
+      organism: 'euk'
+  tmhmm:
+

psot/default_repo/profiles/custom3.yaml

+name: 'custom3'
+info: 'Profile that contains tools for even more testing'
+modules:
+  targetp:
+      organism_group: 'non-plant'
+  signalp:
+      organism: 'euk'
+  tmhmm:
+  hmmer_pfam_a:
+  
+

psot/default_repo/scripts/run_blastp.py

 #!/usr/bin/env python3
 import argparse
-from psot import config
-from os import system
+from os import system,environ
 
-blastp_tool = config.load_config()['tools'].get('blastp', 'blastp')
+def find_tool_path():
+    from psot import config
+    return config.load_config()['tools'].get('blastp', 'blastp')
+
+blastp_tool = ''
+
+if 'INSIDE_CONTAINER' in environ:
+    blastp_tool = 'blastp'
+else:
+    blastp_tool = find_tool_path()
 
 parser = argparse.ArgumentParser(description='Identify homologues in the swissprot database')
 parser.add_argument('--fasta', '-f', required=True, help='A fasta file with aminoacid sequences')

psot/default_repo/scripts/run_ghostx.py

@@ -2,13 +2,23 @@
 
 import argparse
 import re
-from os import system,makedirs,path
-from psot import config
+from os import system,makedirs,path,environ
 import subprocess
 import json
 
-cfg = config.load_config()
-ghostx_tool = cfg['tools'].get('ghostx', 'ghostx')
+def find_tool_path():
+    from psot import config
+    cfg = config.load_config()
+    return cfg['tools'].get('ghostx', 'ghostx'), cfg['helpers_path'] + '/reduce_fasta_headers_to_enumeration.py'
+
+ghostx_tool = ''
+reduce_headers_tool =''
+
+if 'INSIDE_CONTAINER' in environ:
+    ghostx_tool = 'ghostx'
+    reduce_headers_tool = 'reduce_fasta_headers_to_enumeration.py'
+else:
+    ghostx_tool, reduce_headers_tool  = find_tool_path()
 
 parser = argparse.ArgumentParser(description='Identify homologues in the swissprot database')
 parser.add_argument('--fasta', '-f', required=True, help='A fasta file with aminoacid sequences')
@@ -19,7 +29,6 @@ args = parser.parse_args()
 makedirs(args.output, exist_ok=True)
 
 # Swap fasta headers for unique numbers to save ghostx from dealing with complex headers
-reduce_headers_tool = cfg['helpers_path'] +  '/reduce_fasta_headers_to_enumeration.py'
 subprocess.run([reduce_headers_tool, "-f", args.fasta, "-e", args.output + '/enum_headers.tsv'])
 
 # Aproach:
@@ -32,8 +41,8 @@ toolconfig = {
         'database': args.database 
 }
 # find version
-output = subprocess.run([ghostx_tool], stderr=subprocess.PIPE)
-text = output.stderr.decode('ascii') 
+output = subprocess.run([ghostx_tool], stdout=subprocess.PIPE)
+text = output.stdout.decode('ascii') 
 result = re.search('version (.*)', text)
 toolconfig['version'] = result.group(1)
 

psot/default_repo/scripts/run_hmmer.py

 #!/usr/bin/env python3
+
 import argparse
 import json
-from psot import config
-from os import system, makedirs
+from os import system,makedirs,environ
+
+def find_tool_path():
+    from psot import config
+    return config.load_config()['tools'].get('hmmscan', 'hmmscan')
+
+hmmscan_tool = ''
 
-hmmscan_tool = config.load_config()['tools'].get('hmmscan', 'hmmscan')
+if 'INSIDE_CONTAINER' in environ:
+    hmmscan_tool = 'hmmscan'
+else:
+    hmmscan_tool = find_tool_path()
 
 parser = argparse.ArgumentParser(description='Search sequences against a profile database')
 parser.add_argument('--fasta', '-f', required=True, help='A fasta file with aminoacid sequences')

psot/main.py

@@ -29,6 +29,11 @@ def main():
     analyze_parser.add_argument('--debug', '-d', action='store_true', help='Debug mode, computation directory will not be removed after computation')
     analyze_parser.add_argument('--execution_dir', '-e', help='Use the specified execution directory and do not delete it after the computation')
     analyze_parser.add_argument('--use_cluster', '-C', action='store_true', help='Use compute cluster for execution')
+    
+    images = analyze_parser.add_mutually_exclusive_group()
+    images.add_argument('--docker', '-D', action='store_true', help='Use docker image for computation')
+    images.add_argument('--singularity', '-S', action='store_true', help='Use singularity image for computation')
+    
     analyze_parser.set_defaults(func=analyze)
 
     args = parser.parse_args()
@@ -66,6 +71,8 @@ def generate_execution(config, args):
     execution['fasta'] = os.path.abspath(args.fasta)
     execution['output'] = os.path.abspath(args.output)
     execution['install_path'] = config['install_path']
+    execution['docker'] = args.docker
+    execution['singularity'] = args.singularity
     if 'venv' in config:
         execution['venv'] = config['venv']
     if args.execution_dir:

psot/nextflow.py

@@ -244,14 +244,19 @@ def generate_nextflow_config(execution):
     modules = execution['modules']
     
     fragments = []
-    fragments.append('''docker.enabled = true''')
+    
+    if execution['docker']:
+        fragments.append('''docker.enabled = true''')
+    elif execution['singularity']:
+        fragments.append('''singularity.enabled = true''')
+        
     fragments.append('''process { ''')
             
     for m in modules:
         config = {}
         config['id'] = m['id']
         
-        if m['analysis']['container']:
+        if execution['docker'] or execution['singularity'] and 'container' in m['analysis']:
             config['container'] = "container = " + "'" + m['analysis']['container'] + "'"
         else:
             config['container'] = ''