From b2618dd9a78efda75000614a3c9eaac2e6354f29 Mon Sep 17 00:00:00 2001
From: Holger Brandl <brandl@mpi-cbg.de>
Date: Tue, 16 Jun 2015 11:02:54 +0200
Subject: [PATCH] continued star wrapper
---
dge_workflow/dge_utils.sh | 2 +-
dge_workflow/star_align.sh | 44 ++++++++++++++++++++++----------------
2 files changed, 27 insertions(+), 19 deletions(-)
diff --git a/dge_workflow/dge_utils.sh b/dge_workflow/dge_utils.sh
index 069fb0e..9cc7225 100755
--- a/dge_workflow/dge_utils.sh
+++ b/dge_workflow/dge_utils.sh
@@ -165,7 +165,7 @@ wait4jobs .tophatjobs
-dge_bam_correlate .
+dge_bam_correlate . &
## create tophat mapping report
spin.R ${NGS_TOOLS}/dge_workflow/tophat_qc.R .
diff --git a/dge_workflow/star_align.sh b/dge_workflow/star_align.sh
index 636d3b8..1ad3346 100755
--- a/dge_workflow/star_align.sh
+++ b/dge_workflow/star_align.sh
@@ -5,14 +5,23 @@
usage='
Use star to align fastq files against a genome
-Usage: star_align.sh <igenome> <fastq_files>...
+Usage: star_align.sh <igenome> <fastq_files>
Options:
+-c Cache results
'
-#-c Cache results
-eval $(echo "$usage" | ~/bin/docopts/docopts -h - -A dopts : "$@")
-#eval $(echo "$usage" | ~/bin/docopts/docopts -h - : /projects/bioinfo/igenomes/Mus_musculus/Ensembl/GRCm38 /projects/bioinfo/holger/projects/florio_11b_2nd_batch/lanereps_pooled/arhgap11b_1.fastq.gz)
+#eval $(echo "$usage" | ~/bin/docopts/docopts -h - -A dopts : "$@")
+#echo "$usage" | ~/bin/docopts/docopts -h - : "$@"
+#echo "$usage" | ~/bin/docopts/docopts -h - : "hallo dfds"
+#eval $(echo $usage | ~/bin/docopts/docopts -h - : "$@")
+#eval(exit 64)
+eval "$(echo "$usage" | ~/bin/docopts/docopts -h - : "$@")"
+
+# v0.7 style
+#eval $(echo "$usage" | /home/brandl/bin/docopts_v0.7/docopts "hallo")
+
+#eval "$(echo "$usage" | ~/bin/docopts/docopts -h - : /projects/bioinfo/igenomes/Mus_musculus/Ensembl/GRCm38 /projects/bioinfo/holger/projects/florio_11b_2nd_batch/lanereps_pooled/arhgap11b_1.fastq.gz)"
#for fastqFile in ${fastq_files[@]} ; do
# echo processing $fastqFile
@@ -21,34 +30,33 @@ eval $(echo "$usage" | ~/bin/docopts/docopts -h - -A dopts : "$@")
#echo $igenome
-## build index if not present
-
+fastqFiles=${fastq_files[@]}
+#echo $fastqFiles
-
-export star_index="$igenome/Sequence/StarIndex/genome"
+export star_index="${igenome}/Sequence/StarIndex"
export gtfFile="$igenome/Annotation/Genes/genes.gtf"
-head $gtfFile
+#head $gtfFile
if [ ! -f $gtfFile ]; then
>&2 echo "gtf '$gtfFile' does not exis"; exit 1;
fi
-## basic
+## basic usage tutorial
#http://www.homolog.us/blogs/blog/2012/11/02/star-really-kick-ass-rna-seq-aligner/
-if ! -d "${igenome}/Sequence/StarIndex" ]; then
+## build index if not present
+if ! -d "${star_index}" ]; then
mailme "${project}: creating STAR index for $igenome"
-mkdir ${igenome}/Sequence/StarIndex
+mkdir ${star_index}
-cmd="STAR --runMode genomeGenerate --genomeDir ${igenome}/Sequence/StarIndex --genomeFastaFiles ${igenome}/Sequence/WholeGenomeFasta/genome.fa --runThreadN 10"
+cmd="STAR --runMode genomeGenerate --genomeDir ${star_index} --genomeFastaFiles ${igenome}/Sequence/WholeGenomeFasta/genome.fa --runThreadN 10"
#eval $cmd
-#STAR --runMode genomeGenerate --genomeDir ${igenome}/Sequence/StarIndex --genomeFastaFiles ${igenome}/Sequence/Chromosomes/*.fa --runThreadN 10
+#STAR --runMode genomeGenerate --genomeDir ${star_index} --genomeFastaFiles ${igenome}/Sequence/Chromosomes/*.fa --runThreadN 10
mysub "${project}_star_index" "$cmd" -n 5 -R span[hosts=1] -q medium | blockScript
## prevent modification
-chmod -R -w ${igenome}/Sequence/StarIndex
-
+chmod -R -w ${star_index}
fi
@@ -70,7 +78,7 @@ ll $fastqFiles
for fastqFile in $fastqFiles ; do
echo "submitting tophat job for $fastqFile"
- # DEBUG fastqFile=/projects/bioinfo/holger/projects/helin/mouse/trimmed/mouse_big_cyst_rep4_ca.fastq.gz
+ # DEBUG fastqFile=/projects/bioinfo/holger/projects/florio_11b_2nd_batch/lanereps_pooled/arhgap11b_1.fastq.gz
fastqBaseName=$(basename ${fastqFile%%.fastq.gz})
outputdir=$fastqBaseName
@@ -80,7 +88,7 @@ for fastqFile in $fastqFiles ; do
## note --outSAMstrandField intronMotif is required for cuffdiff compatiblity (xs flag)
mysub "${project}__star__${fastqBaseName}" "
# tophat -p6 -G $gtfFile -g1 -o $outputdir $bowtie_gindex $fastqFile
- STAR --genomeDir $star_index --readFilesIn /path/to/read1 $fastqFile --runThreadN 6 --outFileNamePrefix $fastqBaseName --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --sjdbGTFfile
+ STAR --genomeDir $star_index --readFilesIn $fastqFile --runThreadN 6 --readFilesCommand zcat --outFileNamePrefix $fastqBaseName --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --sjdbGTFfile $gtfFile
" -n 5 -R span[hosts=1] -q long | joblist .tophatjobs
done
--
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