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comparison snpEff_2_1a/scripts/distro.sh @ 0:f8eaa3f8194b default tip

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Uploaded snpEff_v2_1a_core.tgz from Pablo Cingolani
author greg
date Fri, 20 Apr 2012 14:47:09 -0400
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1 #!/bin/sh
2
3 #------------------------------------------------------------------------------
4 # Create a zip file for distribution
5 # Note: Only binary data is included (no raw gene info / genomes)
6 #
7 # Pablo Cingolani 2010
8 #------------------------------------------------------------------------------
9
10 VERSION="2_1"
11 VERSION_REV=$VERSION"a"
12 DIR=$HOME/snpEff_$VERSION_REV
13 rm -rvf $DIR
14 mkdir $DIR
15
16 # Copy core files
17 cp snpEff.config snpEff.jar $DIR
18 cp -rvfH galaxy scripts $DIR
19
20 cd $DIR
21 rm -rvf `find . -name "CVS" -type d`
22 cd -
23
24 # Create 'core' zip file
25 cd $HOME
26 ZIP="snpEff_v"$VERSION_REV"_core.zip"
27 rm -f $ZIP 2> /dev/null
28 zip -r $ZIP snpEff_$VERSION_REV
29 cd -
30
31 # Create ZIP file for each database
32 for d in `ls data/*/snpEffectPredictor.bin`
33 do
34 DIR=`dirname $d`
35 GEN=`basename $DIR`
36
37 echo $GEN
38 ZIP="snpEff_v"$VERSION"_"$GEN".zip"
39 zip -r $ZIP data/$GEN/*.bin
40 done
41
42 # Look for missing genomes
43 echo Missing genomes:
44 ls -d data/*/snpEffectPredictor.bin | grep -v genomes | cut -f 2 -d / | sort > genomes_bins.txt
45 ls -d data/* | grep -v genomes | cut -f 2 -d / | sort > genomes_dirs.txt
46 diff genomes_dirs.txt genomes_bins.txt | grep "^<"
47