diff options
Diffstat (limited to 'sci-biology/SEECER/files/run_seecer.sh.patch')
| -rw-r--r-- | sci-biology/SEECER/files/run_seecer.sh.patch | 42 |
1 files changed, 42 insertions, 0 deletions
diff --git a/sci-biology/SEECER/files/run_seecer.sh.patch b/sci-biology/SEECER/files/run_seecer.sh.patch new file mode 100644 index 000000000..a20c7917f --- /dev/null +++ b/sci-biology/SEECER/files/run_seecer.sh.patch @@ -0,0 +1,42 @@ +--- SEECER/bin/run_seecer.sh.old 2013-10-02 18:55:24.000000000 +0200 ++++ SEECER/bin/run_seecer.sh 2017-11-21 16:24:24.065584149 +0100 +@@ -33,6 +33,7 @@ + SeecerStep=1 + LCOUNT=3 + TMPDIR='' ++THREADS=32 + + usage=$(cat << EOF + # This script runs the SEECER pipeline of 4 steps: +@@ -54,11 +55,12 @@ + -j <v> : specify the location of JELLYFISH binary (default = $JF). + -p <v> : specify extra SEECER parameters (default = ''). + -s <v> : specify the starting step ( default = 1). Values = 1,2,3,4. ++ -c <v> : number of threads (default = 32). + -h : help message + EOF + ); + +-while getopts ":j:p:k:s:t:h" opt; do ++while getopts ":j:p:k:s:t:c:h" opt; do + case $opt in + t) + TMPDIR=$OPTARG +@@ -75,6 +77,8 @@ + s) + SeecerStep=$OPTARG + ;; ++ c) ++ THREADS=$OPTARG + \?) + echo "Invalid option: -$OPTARG" >&2 + echo "$usage" +@@ -170,7 +177,7 @@ + then + echo "++ Step 2: Running JELLYFISH to count kmers ..." + echo +- bash "${BINDIR}"run_jellyfish.sh $JF $TMPDIR/counts_${K}_${LCOUNT} $K $LCOUNT $TMPDIR $Read1_N $Read2_N || exit 255 ++ bash "${BINDIR}"run_jellyfish.sh $JF $TMPDIR/counts_${K}_${LCOUNT} $K $LCOUNT $TMPDIR $Read1_N $Read2_N $THREADS || exit 255 + fi; + + if [ ! -r $TMPDIR/counts_${K}_${LCOUNT} ]; |