Commit f864e445 authored by Holger Brandl's avatar Holger Brandl
Browse files

added gff sorting utility

parent 33202806
## tbd
export BIO_BIN_BASE="~/bin"
export PATH=${BIO_BIN_BASE}/igvtools_2.3.91:$PATH
igvsort(){
if [ $# -lt 1 ]; then echo "Usage: igvsort <gfffile>"; return; fi
gffFile=$1
igvtools sort ${gffFile} ${gffFile%%.gff3}.sorted.gff
igvtools index ${gffFile%%.gff3}.sorted.gff
}
export -f igvsort
......@@ -187,3 +187,8 @@ export NGS_TOOLS=/net/mack/lustre/projects/bioinfo/scripts/ngs_tools/dev
source ${NGS_TOOLS}/dge_workflow/dge_utils.sh
dge_create_star_index /local2/igenomes/Mus_Musculus/Ensembl/NCBIM37__ens66_july2015
cd ~/bin
wget http://data.broadinstitute.org/igv/projects/downloads/igvtools_2.3.91.zip
tar xvf igvtools_2.3.91.zip
mv IGVTools igvtools_2.3.91
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