Mercurial > repos > pcingola > snpeff
diff snpEff_2_1a/snpEff_2_1a/scripts/distro.sh @ 3:c052639fa666 default tip
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author | pcingola |
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date | Fri, 20 Apr 2012 11:22:59 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/snpEff_2_1a/scripts/distro.sh Fri Apr 20 11:22:59 2012 -0400 @@ -0,0 +1,47 @@ +#!/bin/sh + +#------------------------------------------------------------------------------ +# Create a zip file for distribution +# Note: Only binary data is included (no raw gene info / genomes) +# +# Pablo Cingolani 2010 +#------------------------------------------------------------------------------ + +VERSION="2_1" +VERSION_REV=$VERSION"a" +DIR=$HOME/snpEff_$VERSION_REV +rm -rvf $DIR +mkdir $DIR + +# Copy core files +cp snpEff.config snpEff.jar $DIR +cp -rvfH galaxy scripts $DIR + +cd $DIR +rm -rvf `find . -name "CVS" -type d` +cd - + +# Create 'core' zip file +cd $HOME +ZIP="snpEff_v"$VERSION_REV"_core.zip" +rm -f $ZIP 2> /dev/null +zip -r $ZIP snpEff_$VERSION_REV +cd - + +# Create ZIP file for each database +for d in `ls data/*/snpEffectPredictor.bin` +do + DIR=`dirname $d` + GEN=`basename $DIR` + + echo $GEN + ZIP="snpEff_v"$VERSION"_"$GEN".zip" + zip -r $ZIP data/$GEN/*.bin +done + +# Look for missing genomes +echo Missing genomes: +ls -d data/*/snpEffectPredictor.bin | grep -v genomes | cut -f 2 -d / | sort > genomes_bins.txt +ls -d data/* | grep -v genomes | cut -f 2 -d / | sort > genomes_dirs.txt +diff genomes_dirs.txt genomes_bins.txt | grep "^<" +