finished snATAC demux

epigen-UCSD · Jan 16, 2019 · 0d9de68 · 0d9de68
1 parent 297f037
commit 0d9de68
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Showing 3 changed files with 21 additions and 13 deletions.
diff --git a/nextseq_app/views.py b/nextseq_app/views.py
@@ -681,8 +681,14 @@ def DemultiplexingView(request, run_pk):
         RunInfo.objects.filter(pk=run_pk).update(jobstatus='JobSubmitted')
 
         # runBcl2fastq
-        cmd1 = './utility/runBcl2fastq.sh ' + runinfo.Flowcell_ID + \
-            ' ' + basedirname + ' ' + request.user.email
+        if runinfo.experiment_type == 'S2':
+            cmd1 = './utility/runDemuxSnATAC.sh ' + runinfo.Flowcell_ID + \
+                ' ' + basedirname + ' ' + request.user.email
+        else:
+            cmd1 = './utility/runBcl2fastq.sh ' + runinfo.Flowcell_ID + \
+                ' ' + basedirname + ' ' + request.user.email
+        print(cmd1)
+
         p = subprocess.Popen(
             cmd1, shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
         # thisjobid=p.pid
@@ -715,8 +721,8 @@ def DemultiplexingView2(request, run_pk):
             break
     # print(data)
     if 'is_direxists' in data:
-        shutil.rmtree(os.path.join(basedirname, 'Data/Fastqs'))
-        os.mkdir(os.path.join(basedirname, 'Data/Fastqs'))
+        #shutil.rmtree(os.path.join(basedirname, 'Data/Fastqs'))
+        #os.mkdir(os.path.join(basedirname, 'Data/Fastqs'), exist_ok=True)
 
         samples_list = runinfo.librariesinrun_set.all()
 
@@ -817,8 +823,14 @@ def DemultiplexingView2(request, run_pk):
         RunInfo.objects.filter(pk=run_pk).update(jobstatus='JobSubmitted')
 
         # runBcl2fastq
-        cmd1 = './utility/runBcl2fastq.sh ' + runinfo.Flowcell_ID + \
-            ' ' + basedirname + ' ' + request.user.email
+        if runinfo.experiment_type == 'S2':
+            cmd1 = './utility/runDemuxSnATAC.sh ' + runinfo.Flowcell_ID + \
+                ' ' + basedirname + ' ' + request.user.email
+
+        else:
+            cmd1 = './utility/runBcl2fastq.sh ' + runinfo.Flowcell_ID + \
+                ' ' + basedirname + ' ' + request.user.email
+        print(cmd1)
         p = subprocess.Popen(
             cmd1, shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
         # thisjobid=p.pid

diff --git a/utility/runDemuxSnATAC.sh b/utility/runDemuxSnATAC.sh
@@ -1,11 +1,7 @@
 #!/bin/bash
 
-## cmd1: qsub bcl2fastq job
+## cmd1: qsub job from tscc 
 flowcell=$1; rundir=$2; useremail=$3
-cmd1="qsub -M $useremail -v flowcell_id=$flowcell,run_dir=$rundir \$(which runBcl2fastq.pbs)"
+cmd1="qsub -k oe  -M $useremail -v flowcell_id=$flowcell,run_dir=$rundir \$(which runDemuxSnATAC.pbs)"
 ssh [email protected] $cmd1
 
-
-## cmd2: 
-
-
diff --git a/utility/runSetQC.sh b/utility/runSetQC.sh
@@ -24,7 +24,7 @@ awk -v FS='\t' '(NR>1&&$4=="No"){print $1,$2}' $STATUS_FILE > $RUN_LOG_PIP
 n_libs=$(wc -l $RUN_LOG_PIP | awk '{print $1}')
 if [ $n_libs -gt 0 ]
 then
-    cmd1="qsub -v samples=${RUN_LOG_PIP} -t 0-$[n_libs-1] -M $USER_EMAIL -q home-epigen -l walltime=16:00:00 \$(which runPipeline_fastq.pbs)"
+    cmd1="qsub -v samples=${RUN_LOG_PIP} -t 0-$[n_libs-1] -M $USER_EMAIL -q home-epigen -l walltime=16:00:00,pmem=8gb \$(which runPipeline_fastq.pbs)"
     job1=$(ssh [email protected] $cmd1)
     python updateLibrariesSetQC.py -s '1' -id $SET_ID # process libs
     cmd2="qsub -W depend=afterokarray:$job1 -M $USER_EMAIL -v set_id=$SET_ID,type=$TYPE  \$(which runSetQC.pbs)"