Mercurial > repos > davidvanzessen > argalaxy_tools
changeset 2:d8d61e65dfd5 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Thu, 23 Jul 2015 10:29:44 -0400 |
| parents | c06d0df9ec44 |
| children | c7c7000de220 |
| files | experimental_design.xml imgt_loader/imgt_loader.sh |
| diffstat | 1 files changed, 11 insertions(+), 3 deletions(-) [+] |
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--- a/imgt_loader/imgt_loader.sh Thu Jul 16 08:39:04 2015 -0400 +++ b/imgt_loader/imgt_loader.sh Thu Jul 23 10:29:44 2015 -0400 @@ -11,6 +11,7 @@ gzipType="gzip compressed" zipType="Zip archive" rarType="RAR archive" +zxType="XZ compressed data" if [[ "$f" == *"$zip7Type"* ]]; then echo "7-zip" @@ -22,21 +23,21 @@ then echo "tar archive" echo "Trying: tar xvf $input -C $PWD/files/" - tar xvf $input -C $PWD/$name/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 + 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 + tar -xvzf $input -C $PWD/$name/files fi if [[ "$f" == *"$zipType"* ]] @@ -52,6 +53,13 @@ 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