From 6a530e75237418873bf6f03da7421a28b46ce81f Mon Sep 17 00:00:00 2001
From: Holger Brandl <brandl@mpi-cbg.de>
Date: Tue, 11 Nov 2014 18:02:54 +0100
Subject: [PATCH] cont dge automation
---
bash/lsf_rna_seq.sh | 66 +++++++++++++++++++++++++++++++++++++++------
1 file changed, 58 insertions(+), 8 deletions(-)
diff --git a/bash/lsf_rna_seq.sh b/bash/lsf_rna_seq.sh
index 6223369..2d95e5e 100644
--- a/bash/lsf_rna_seq.sh
+++ b/bash/lsf_rna_seq.sh
@@ -1,6 +1,55 @@
-#http://wiki.bash-hackers.org/howto/getopts_tutorial
+## create fastq report for all fastq and fastq.gz files in the current directory
+dge_fastqc(){
+
+while getopts "o:" curopt; do
+ case $curopt in
+ o) outputDir=$OPTARG;
+ esac
+done
+shift $(($OPTIND - 1))
+
+fastqFiles=$*
+
+#if [ -z "$fastqFiles" ]; then
+if [ $# -lt 1 ]; then
+ echo "Usage: dge_fastqc [-o <output_directory>] [<fastq.gz file>]+" >&2 ; return;
+fi
+
+## use default directory if not specified
+if [ -z "$outputDir" ]; then
+ outputDir="fastqc_reports"
+fi
+
+if [ ! -d "$outputDir" ]; then
+ echo "creating output directory '$outputDir'"
+ mkdir $outputDir
+fi
+
+
+for fastqFile in $fastqFiles ; do
+ echo "fastqcing $fastqFile"
+ if [ ! -f $fastqFile ]; then
+ continue;
+ fi
+
+
+ mysub "fastqc__$(basename $fastqFile)" "fastqc -j /sw/bin/java -o $outputDir -f fastq $fastqFile" -q medium | joblist .fastqc_jobs
+done
+
+
+wait4jobs .fastqc_jobs
+
+mailme "fastqc done for $outputDir"
+
+# todo create some summary report here
+}
+export -f dge_fastqc
+
+
+
+#http://wiki.bash-hackers.org/howto/getopts_tutorial
dge_tophat_se(){
# http://stackoverflow.com/questions/18414054/bash-getopts-reading-optarg-for-optional-flags
@@ -13,20 +62,18 @@ done
shift $(($OPTIND - 1))
-if [ -z "$IGENOME" ] || [ $# -eq 1 ];
+fastqFiles=$*
+
+if [ -z "$IGENOME" ] || [ -z "$fastqFiles" ];
then echo "Usage: dge_tophat_se -i <path to igenome> [<fastq.gz file>]+" >&2 ; return;
fi
-fastqFiles=$*
-echo "running tophat using igenome $IGENOME for the following files"
-echo $
-export bowtie_gindex="$IGENOME_BASE/Sequence/Bowtie2Index/genome"
-export gtfFile="$IGENOME_BASE/Annotation/Genes/genes.gtf"
+export bowtie_gindex="$IGENOME/Sequence/Bowtie2Index/genome"
+export gtfFile="$IGENOME/Annotation/Genes/genes.gtf"
#head $gtfFile
-
if [ ! -f $gtfFile ]; then
>&2 echo "gtf '$gtfFile' does not exis"; return;
fi
@@ -35,6 +82,9 @@ if [ -z "$(which tophat)" ]; then
>&2 echo "no tomcat binary in PATH"; return;
fi
+
+echo "running tophat using igenome '$IGENOME' for the following files"
+
#fastqFiles=$(ls $baseDir/treps_pooled/*fastq.gz)
for fastqFile in $fastqFiles ; do
--
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