Mercurial > repos > davidvanzessen > shm_csr
changeset 72:c787e79e8b90 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Tue, 05 Feb 2019 03:26:41 -0500 |
| parents | 2649a821162d |
| children | 825c07055d73 |
| files | change_o/define_clones.sh change_o/makedb.sh shm_csr.xml wrapper.sh |
| diffstat | 4 files changed, 6 insertions(+), 11 deletions(-) [+] |
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--- a/change_o/define_clones.sh Thu Jan 31 05:53:59 2019 -0500 +++ b/change_o/define_clones.sh Tue Feb 05 03:26:41 2019 -0500 @@ -21,9 +21,7 @@ output=${10} output2=${11} - python3 $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 + DefineClones.py -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 @@ -31,9 +29,7 @@ output=$4 output2=$5 - python3 $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 + 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/change_o/makedb.sh Thu Jan 31 05:53:59 2019 -0500 +++ b/change_o/makedb.sh Tue Feb 05 03:26:41 2019 -0500 @@ -29,9 +29,7 @@ echo "makedb: $PWD/outdir" -python3 $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 +MakeDb.py imgt -i $input --outdir $PWD/outdir --outname output $noparse $scores $regions mv $PWD/outdir/output_db-pass.tab $output
--- a/shm_csr.xml Thu Jan 31 05:53:59 2019 -0500 +++ b/shm_csr.xml Tue Feb 05 03:26:41 2019 -0500 @@ -9,6 +9,7 @@ <requirement type="package" version="0.5.0">r-scales</requirement> <requirement type="package" version="3.4_5">r-seqinr</requirement> <requirement type="package" version="1.11.4">r-data.table</requirement> + <requirement type="package" version="0.4.5">changeo</requirement> </requirements> <command interpreter="bash"> #if str ( $filter_unique.filter_unique_select ) == "remove":
--- a/wrapper.sh Thu Jan 31 05:53:59 2019 -0500 +++ b/wrapper.sh Tue Feb 05 03:26:41 2019 -0500 @@ -72,7 +72,7 @@ echo "---------------- class identification ----------------" echo "---------------- class identification ----------------<br />" >> $log -python2 $dir/gene_identification.py --input $PWD/summary.txt --output $outdir/identified_genes.txt +python $dir/gene_identification.py --input $PWD/summary.txt --output $outdir/identified_genes.txt echo "---------------- merge_and_filter.r ----------------" echo "---------------- merge_and_filter.r ----------------<br />" >> $log @@ -198,7 +198,7 @@ echo "---------------- shm_csr.py ----------------" echo "---------------- shm_csr.py ----------------<br />" >> $log -python2 $dir/shm_csr.py --input $outdir/merged.txt --genes $classes --empty_region_filter "${empty_region_filter}" --output $outdir/hotspot_analysis.txt +python $dir/shm_csr.py --input $outdir/merged.txt --genes $classes --empty_region_filter "${empty_region_filter}" --output $outdir/hotspot_analysis.txt echo "---------------- aa_histogram.r ----------------" echo "---------------- aa_histogram.r ----------------<br />" >> $log