Mercurial > repos > davidvanzessen > change_o
changeset 2:6f57d43a1f4c draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Thu, 11 Aug 2016 07:40:36 -0400 |
| parents | 326165da9ece |
| children | 5173675d0d10 |
| files | create_germlines.sh define_clones.sh makedb.sh |
| diffstat | 3 files changed, 8 insertions(+), 8 deletions(-) [+] |
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--- a/create_germlines.sh Thu Aug 04 08:59:47 2016 -0400 +++ b/create_germlines.sh Thu Aug 11 07:40:36 2016 -0400 @@ -16,7 +16,7 @@ mkdir $PWD/outdir -/home/galaxy/anaconda3/bin/python $dir/CreateGermlines.py -d $PWD/input.tab -r $dir/IMGT_Human_IGH[VDJ].fasta --outdir $PWD/outdir --outname output -g $type $cloned -#/data/users/david/anaconda3/bin/python $dir/CreateGermlines.py -d $PWD/input.tab -r $dir/IMGT_Human_IGH[VDJ].fasta --outdir $PWD/outdir --outname output -g $type $cloned +#/home/galaxy/anaconda3/bin/python $dir/CreateGermlines.py -d $PWD/input.tab -r $dir/IMGT_Human_IGH[VDJ].fasta --outdir $PWD/outdir --outname output -g $type $cloned +/data/users/david/anaconda3/bin/python $dir/CreateGermlines.py -d $PWD/input.tab -r $dir/IMGT_Human_IGH[VDJ].fasta --outdir $PWD/outdir --outname output -g $type $cloned mv $PWD/outdir/output_germ-pass.tab $output
--- a/define_clones.sh Thu Aug 04 08:59:47 2016 -0400 +++ b/define_clones.sh Thu Aug 11 07:40:36 2016 -0400 @@ -21,8 +21,8 @@ output=${10} output2=${11} - #/data/users/david/anaconda3/bin/python $dir/DefineClones.py bygroup -d $PWD/input.tab --nproc 4 --outdir $PWD/outdir --outname output --mode $mode --act $act --model $model --dist $dist --norm $norm --sym $sym --link $link - /home/galaxy/anaconda3/bin/python $dir/DefineClones.py bygroup -d $PWD/input.tab --nproc 4 --outdir $PWD/outdir --outname output --mode $mode --act $act --model $model --dist $dist --norm $norm --sym $sym --link $link + /data/users/david/anaconda3/bin/python $dir/DefineClones.py bygroup -d $PWD/input.tab --nproc 4 --outdir $PWD/outdir --outname output --mode $mode --act $act --model $model --dist $dist --norm $norm --sym $sym --link $link + #/home/galaxy/anaconda3/bin/python $dir/DefineClones.py bygroup -d $PWD/input.tab --nproc 4 --outdir $PWD/outdir --outname output --mode $mode --act $act --model $model --dist $dist --norm $norm --sym $sym --link $link Rscript $dir/define_clones.r $PWD/outdir/output_clone-pass.tab $output2 2>&1 else @@ -30,8 +30,8 @@ output=$4 output2=$5 - #/data/users/david/anaconda3/bin/python $dir/DefineClones.py hclust -d $PWD/input.tab --nproc 4 --outdir $PWD/outdir --outname output --method $method - /home/galaxy/anaconda3/bin/python $dir/DefineClones.py hclust -d $PWD/input.tab --nproc 4 --outdir $PWD/outdir --outname output --method $method + /data/users/david/anaconda3/bin/python $dir/DefineClones.py hclust -d $PWD/input.tab --nproc 4 --outdir $PWD/outdir --outname output --method $method + #/home/galaxy/anaconda3/bin/python $dir/DefineClones.py hclust -d $PWD/input.tab --nproc 4 --outdir $PWD/outdir --outname output --method $method Rscript $dir/define_clones.r $PWD/outdir/output_clone-pass.tab $output2 2>&1 fi
--- a/makedb.sh Thu Aug 04 08:59:47 2016 -0400 +++ b/makedb.sh Thu Aug 11 07:40:36 2016 -0400 @@ -27,7 +27,7 @@ mkdir $PWD/outdir -#/data/users/david/anaconda3/bin/python $dir/MakeDb.py imgt -i $input --outdir $PWD/outdir --outname output $noparse $scores $regions -/home/galaxy/anaconda3/bin/python $dir/MakeDb.py imgt -i $input --outdir $PWD/outdir --outname output $noparse $scores $regions +/data/users/david/anaconda3/bin/python $dir/MakeDb.py imgt -i $input --outdir $PWD/outdir --outname output $noparse $scores $regions +#/home/galaxy/anaconda3/bin/python $dir/MakeDb.py imgt -i $input --outdir $PWD/outdir --outname output $noparse $scores $regions mv $PWD/outdir/output_db-pass.tab $output