Merge pull request #359 from CGATOxford/AC-conda_env_pe

Ac conda env pe
CGATOxford · Oct 23, 2017 · 09667b6 · 09667b6
2 parents f756af3 + 7aca537
commit 09667b6
Show file tree

Hide file tree

Showing 3 changed files with 12 additions and 7 deletions.
diff --git a/CGATPipelines/PipelinePeakcalling.py b/CGATPipelines/PipelinePeakcalling.py
@@ -1798,7 +1798,8 @@ def callPeaks(self, infile, outfile, controlfile=None, conda_env=None):
                 'bamToBed -i %(controlfile)s \
                 > %(workdir)s/control.bed' % locals())
             statement.append("cd %(workdir)s" % locals())
-            statement.append('''SICER.sh . foreground.bed control.bed \
+            statement.append('''%(conda_env)s &&
+            SICER.sh . foreground.bed control.bed \
             . %(genome)s
             %(redundancy_threshold)s
             %(window_size)s
@@ -1810,7 +1811,8 @@ def callPeaks(self, infile, outfile, controlfile=None, conda_env=None):
 
         else:
             statement.append('cd%(workdir)s')
-            statement.append('''SICER-rb.sh .foreground.bed . %(genome)s
+            statement.append('''%(conda_env)s &&
+            SICER-rb.sh .foreground.bed . %(genome)s
             %(redundancy_threshold)s
             %(window_size)s
             %(fragment_size)s

diff --git a/CGATPipelines/pipeline_peakcalling.py b/CGATPipelines/pipeline_peakcalling.py
@@ -887,7 +887,7 @@ def estimateInsertSize(infile, outfile):
                                            PARAMS['paired_end'],
                                            PARAMS['insert_alignments'],
                                            PARAMS['insert_macs2opts'],
-                                           PARAMS['python2_sourcecommand'])
+                                           PARAMS['python2_macs2'])
 
 
 @merge(estimateInsertSize, "insert_sizes.tsv")
@@ -973,7 +973,7 @@ def callMacs2peaks(infiles, outfile):
                                  PARAMS['macs2_idrsuffix'],
                                  PARAMS['macs2_idrcol'],
                                  PARAMS['macs2_broad_peak'],
-                                 PARAMS['python2_sourcecommand'])
+                                 PARAMS['python2_macs2'])
     P.run()
     peakcaller.summarise(outfile)
 
@@ -1044,7 +1044,8 @@ def callNarrowerPeaksWithSicer(infiles, outfile):
                                  idr=PARAMS['IDR_run'],
                                  idrc=PARAMS['sicer_idrkeeppeaks'],
                                  idrcol=PARAMS['sicer_idrcol'],
-                                 broad_peak=0)
+                                 broad_peak=0,
+                                 conda_env=PARAMS['python2_sicer'])
 
     P.run()
     peakcaller.summarise(outfile, mode="narrow")
@@ -1116,7 +1117,8 @@ def callBroaderPeaksWithSicer(infiles, outfile):
                                  idr=PARAMS['IDR_run'],
                                  idrc=PARAMS['sicer_idrkeeppeaks'],
                                  idrcol=PARAMS['sicer_idrcol'],
-                                 broad_peak=1)
+                                 broad_peak=1,
+                                 conda_env=PARAMS['python2_sicer'])
 
     P.run()
     peakcaller.summarise(outfile, mode="broad")

diff --git a/CGATPipelines/pipeline_peakcalling/pipeline.ini b/CGATPipelines/pipeline_peakcalling/pipeline.ini
@@ -158,7 +158,8 @@ strip=1
 # this sources the python2 conda environment - this is required to run the
 # macs2 software
 # outside of CGAT a different command would be needed! 
-sourcecommand=PATH=/ifs/apps/conda-envs/envs/macs2/bin;CONDA_PREFIX=/ifs/apps/conda-envs/envs/macs2
+macs2=PATH=/ifs/apps/conda-envs/envs/macs2/bin;CONDA_PREFIX=/ifs/apps/conda-envs/envs/macs2
+sicer=export PATH=/usr/local/bin:/usr/bin:/bin:/ifs/apps/conda-envs/envs/sicer/bin:/ifs/apps/bio/sicer-1.1:/ifs/apps/bio/sicer-1.1/utility && export CONDA_PREFIX=/ifs/apps/conda-envs/envs/sicer && export PYTHONPATH=/ifs/apps/bio/sicer-1.1/lib:/ifs/apps/conda-envs/envs/sicer/lib/python2.6/site-packages:/ifs/apps/conda-envs/envs/sicer/lib/python2.6
 unsourcecommand=
 
 [insert]