Merge branch 'devel' into 'master'

Devel

Closes #30

See merge request !18

blast/pBlast.eb

@@ -12,14 +12,16 @@ easyblock   = 'Binary'
 sources     = ['./parallel_BLAST/LA_Wrapper',
                './parallel_BLAST/cleanup.sh',
                './parallel_BLAST/blast_wrap.sh',
-               './parallel_BLAST/splitter.py']
+               './parallel_BLAST/splitter.py',
+               './parallel_BLAST/stage_in.sh']
 
 unpack_sources = False
 
 files_to_copy = ['LA_Wrapper',
                  'cleanup.sh',
                  'blast_wrap.sh',
-                 'splitter.py']
+                 'splitter.py',
+                 'stage_in.sh']
 
 postinstallcmds = ['mv %(installdir)s/parallel_BLAST/* %(installdir)s && rmdir %(installdir)s/parallel_BLAST']
 

blast/parallel_BLAST/blast_wrap.sh

@@ -4,7 +4,10 @@ function cmdfilewriter()
 cat <<EOF > $cmdfile
 #!/bin/bash
   module purge
+  #TODO: find a solution for the bug in BLAST+ AND to select the version by hand
   module load bio/BLAST+/2.9.0-gompi-2019a
+  #module load bio/BLAST+/2.7.1-foss-2018a
+
   # are we done?
   source ${SCRIPT_PATH}/cleanup.sh
   if [ \$1 = "done" ]; then
@@ -16,15 +19,20 @@ cat <<EOF > $cmdfile
   tmp_out=${JOBDIR}/\$outfname
   trap "rm -f \$tmp_out" EXIT
   START_BLAST=\$(date +%s)
-  $BLASTEXE -num_threads $SLURM_CPUS_PER_TASK -db $DATABASE $BLASTPARAMS -query \$1 -out \$tmp_out
+  $_arg_executable -num_threads $SLURM_CPUS_PER_TASK -db $DATABASE $BLASTPARAMS -query \$1 -out \$tmp_out
+  success=\$?
   END_BLAST=\$(date +%s)
   elapsed=\$(bc <<< "scale=1; \$((\$END_BLAST - \$START_BLAST))/60")
-  echo "Elapsed: \$elapsed"
+  #echo "Elapsed for '\$1': \$elapsed"
   
-  # compress, when done
-  gzip \$tmp_out
-
-  # copy back, when ready
-  mv \${tmp_out}.gz ./output/\${outfname}.gz
+  # only proceed, when ready
+  if [ \$success -eq 0 ]; then
+     # compress, when done
+     gzip \$tmp_out
+     # copy back, when ready
+     mv \${tmp_out}.gz ./output/\${outfname}.gz
+  fi
+  # we only consider the blast exit code for the total exit code
+  exit \$success
 EOF
 }

blast/parallel_BLAST/splitter.py

 #!/usr/bin/env python
 
-# dummy line to introduce a line break
-import pip
-# will take little time, if dependency is already satisfied
-pip.main(['install', 'biopython'])
-
 from Bio import SeqIO
 import sys
 import os
@@ -22,7 +17,7 @@ batch = list()
 for pos, entry in enumerate(record_iter):
     if pos == 0:
         group += 1
-        filename = 'group_%5d.fasta' % group
+        filename = 'group_%05d.fasta' % group
         handle = open(os.path.join('scratch', filename), 'w')
     if (pos % nlines == 0 and pos != 0):
         count = SeqIO.write(batch, handle, 'fasta')
@@ -30,10 +25,10 @@ for pos, entry in enumerate(record_iter):
         handle.close()
         batch = list()
         group += 1
-        filename = 'group_%s.fasta' % group
+        filename = 'group_%05d.fasta' % group
         handle = open(os.path.join('scratch', filename), 'w')
     batch.append(entry)
 # take care of the rest
 count = SeqIO.write(batch, handle, 'fasta')
-print('Wrote %s records to %s' % (count, filename))
+#print('Wrote %s records to %s' % (count, filename))
 handle.close()

blast/parallel_BLAST/stage_in.sh

@@ -4,12 +4,9 @@ cat <<EOF > $stagefile
 #!/bin/bash
 target=/localscratch/$SLURM_JOB_ID/ramdisk
 cd \$target
-for fname in \$(find ${DATABASEPATH} -type f ); do
-    #suffix=\${fname#*.}
-    outfile=\$(basename \${fname})
-    cp -L \$fname \$outfile 
-done
+parallel -j 4 cp {} {/} ::: \$(find -L ${DATABASEPATH} -type f ) 
 cd -
+wait
 EOF
 }
 

trim_filter/parallel_QCTools/QCWrapper

@@ -534,7 +534,7 @@ if [ $_arg_paired -eq 1 ]; then
     if [[ ${samples[0]} == *"_R1"* || ${samples[0]} == *"_R2"* ]]; then
         first='_R1'
         second='_R2'
-    elif [[ ${samples[0]} == *"_1"* ]]; then
+    elif [[ ${samples[0]} == *"_1"* ]] || [[ ${samples[0]} == *"_2"* ]]; then
         first='_1'
         second='_2'
     else