started better automation model for rna-seq

bash/lsf_rna_seq.sh

+
+#http://wiki.bash-hackers.org/howto/getopts_tutorial
+
+dge_tophat_se(){
+
+# http://stackoverflow.com/questions/18414054/bash-getopts-reading-optarg-for-optional-flags
+
+while getopts "i:" curopt; do
+    case $curopt in
+    i) IGENOME=$OPTARG;
+    esac
+done
+shift $(($OPTIND - 1))
+
+
+if [ -z "$IGENOME" ] || [ $# -eq 1 ];
+     then echo "Usage: dge_tophat_se -i <path to igenome> [<fastq.gz file>]+" >&2 ; return;
+fi
+
+fastqFiles=$*
+
+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"
+#head $gtfFile
+
+
+if [ ! -f $gtfFile ]; then
+    >&2 echo "gtf '$gtfFile' does not exis"; return;
+fi
+
+if [ -z "$(which tophat)" ]; then
+    >&2 echo "no tomcat binary in PATH"; return;
+fi
+
+#fastqFiles=$(ls $baseDir/treps_pooled/*fastq.gz)
+
+for fastqFile in $fastqFiles ; do
+    echo "submitting tophat job for $fastqFile"
+
+    # DEBUG fastqFile=/projects/bioinfo/holger/projects/eric/trimmed/a1_ca.fastq.gz
+    fastqBaseName=$(basename ${fastqFile%%.fastq.gz})
+    outputdir=$fastqBaseName
+
+    ## uniquely mapping reads only:   http:/seqanswers.com/forums/showthread.php?s=93da11109ae12a773a128a637d69defe&t=3464
+#    mysub "${project}__tophat__${fastqBaseName}" "
+#    tophat -p6  -G $gtfFile -g1 -o $outputdir $bowtie_gindex $fastqFile
+#
+#    mv $outputdir/accepted_hits.bam $outputdir/$(basename $outputdir).bam
+#    samtools index $outputdir/$(basename $outputdir).bam
+#    " -n 5 -R span[hosts=1] -q long | joblist .tophatjobs
+done
+
+wait4jobs .tophatjobs
+
+## create tophat mapping report
+source <(curl https://dl.dropboxusercontent.com/u/113630701/datautils/bash/bioinfo_utils.sh 2>&1 2>/dev/null)
+TophatMappingReport
+
+
+}
+
+# dge_tophat_se
+# dge_tophat_se -i
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