Mercurial > repos > davidvanzessen > argalaxy_tools
view imgt_loader/imgt_loader.sh @ 1:90a05ff900db draft
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author | davidvanzessen |
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date | Mon, 05 Sep 2016 04:46:06 -0400 (2016-09-05) |
parents | afe85eb6572e |
children | 9185c3dfc679 |
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#!/bin/bash input=$1 output=$2 name=$3 dir="$(cd "$(dirname "$0")" && pwd)" mkdir -p $PWD/$name/files f=$(file $input) zip7Type="7-zip archive" tarType="tar archive" bzip2Type="bzip2 compressed" gzipType="gzip compressed" zipType="Zip archive" rarType="RAR archive" zxType="XZ compressed data" if [[ "$f" == *"$zip7Type"* ]]; then echo "7-zip" echo "Trying: 7za e $input -o$PWD/files/" 7za e $input -o$PWD/$name/files fi if [[ "$f" == *"$tarType"* ]] then echo "tar archive" echo "Trying: tar xvf $input -C $PWD/files/" tar -xvf $input -C $PWD/$name/files fi if [[ "$f" == *"$bzip2Type"* ]] then echo "bzip2 compressed data" echo "Trying: tar jxf $input -C $PWD/files/" tar -jxf $input -C $PWD/$name/files fi if [[ "$f" == *"$gzipType"* ]] then echo "gzip compressed data" echo "Trying: tar xvzf $input -C $PWD/files/" tar -xvzf $input -C $PWD/$name/files fi if [[ "$f" == *"$zipType"* ]] then echo "Zip archive" echo "Trying: unzip $input -d $PWD/files/" unzip $input -d $PWD/$name/files > $PWD/unziplog.log fi if [[ "$f" == *"$rarType"* ]] then echo "RAR archive" echo "Trying: unrar e $input $PWD/files/" unrar e $input $PWD/$name/files fi if [[ "$f" == *"$zxType"* ]] then echo "xz compressed data" echo "Trying: tar -xJf $input -C $PWD/files/" tar xJf $input -C $PWD/$name/files fi find $PWD/$name/files -iname "1_*" -exec cat {} + > $PWD/$name/summ.txt find $PWD/$name/files -iname "5_*" -exec cat {} + > $PWD/$name/aa.txt find $PWD/$name/files -iname "6_*" -exec cat {} + > $PWD/$name/junction.txt #python $dir/imgt_loader.py --summ $PWD/$name/summ.txt --aa $PWD/$name/aa.txt --junction $PWD/$name/junction.txt --output $output Rscript --verbose $dir/imgt_loader.r $PWD/$name/summ.txt $PWD/$name/aa.txt $PWD/$name/junction.txt $output 2>&1