| Previous changeset 81:b6f9a640e098 (2021-02-19) Next changeset 83:729738462297 (2021-09-15) |
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Commit message:
Uploaded |
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modified:
.gitattributes change_o/define_clones.sh change_o/makedb.sh |
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added:
change_o/lr.txt |
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| diff -r b6f9a640e098 -r a103134ee6e0 .gitattributes --- a/.gitattributes Fri Feb 19 15:10:54 2021 +0000 +++ b/.gitattributes Thu Feb 25 10:32:32 2021 +0000 |
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| @@ -1,2 +1,4 @@ # Auto detect text files and perform LF normalization * text=auto +# Convert to LF line endings on checkout. +*.sh text eol=lf \ No newline at end of file |
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| diff -r b6f9a640e098 -r a103134ee6e0 change_o/define_clones.sh --- a/change_o/define_clones.sh Fri Feb 19 15:10:54 2021 +0000 +++ b/change_o/define_clones.sh Thu Feb 25 10:32:32 2021 +0000 |
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| @@ -1,39 +1,40 @@ -#!/bin/bash -dir="$(cd "$(dirname "$0")" && pwd)" - -#define_clones.sh $input $noparse $scores $regions $out_file - -type=$1 -input=$2 - -mkdir -p $PWD/outdir - -cp $input $PWD/input.tab #file has to have a ".tab" extension - -if [ "bygroup" == "$type" ] ; then - mode=$3 - act=$4 - model=$5 - norm=$6 - sym=$7 - link=$8 - dist=$9 - output=${10} - output2=${11} - - 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 - method=$3 - output=$4 - output2=$5 - - 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 - -cp $PWD/outdir/output_clone-pass.tab $output - -rm -rf $PWD/outdir/ +#!/bin/bash +# something to make it commit, with unix line ends +dir="$(cd "$(dirname "$0")" && pwd)" + +#define_clones.sh $input $noparse $scores $regions $out_file + +type=$1 +input=$2 + +mkdir -p $PWD/outdir + +cp $input $PWD/input.tab #file has to have a ".tab" extension + +if [ "bygroup" == "$type" ] ; then + mode=$3 + act=$4 + model=$5 + norm=$6 + sym=$7 + link=$8 + dist=$9 + output=${10} + output2=${11} + + 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 + method=$3 + output=$4 + output2=$5 + + 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 + +cp $PWD/outdir/output_clone-pass.tab $output + +rm -rf $PWD/outdir/ |
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| diff -r b6f9a640e098 -r a103134ee6e0 change_o/makedb.sh --- a/change_o/makedb.sh Fri Feb 19 15:10:54 2021 +0000 +++ b/change_o/makedb.sh Thu Feb 25 10:32:32 2021 +0000 |
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| @@ -1,36 +1,36 @@ -#!/bin/bash -dir="$(cd "$(dirname "$0")" && pwd)" - -input=$1 -noparse=$2 -scores=$3 -regions=$4 -output=$5 - -if [ "true" == "$noparse" ] ; then - noparse="--noparse" -else - noparse="" -fi - -if [ "true" == "$scores" ] ; then - scores="--scores" -else - scores="" -fi - -if [ "true" == "$regions" ] ; then - regions="--regions" -else - regions="" -fi - -mkdir $PWD/outdir - -echo "makedb: $PWD/outdir" - -MakeDb.py imgt -i $input --outdir $PWD/outdir --outname output $noparse $scores $regions - -mv $PWD/outdir/output_db-pass.tab $output - -rm -rf $PWD/outdir/ +#!/bin/bash +dir="$(cd "$(dirname "$0")" && pwd)" + +input=$1 +noparse=$2 +scores=$3 +regions=$4 +output=$5 + +if [ "true" == "$noparse" ] ; then + noparse="--noparse" +else + noparse="" +fi + +if [ "true" == "$scores" ] ; then + scores="--scores" +else + scores="" +fi + +if [ "true" == "$regions" ] ; then + regions="--regions" +else + regions="" +fi + +mkdir $PWD/outdir + +echo "makedb: $PWD/outdir" + +MakeDb.py imgt -i $input --outdir $PWD/outdir --outname output $noparse $scores $regions + +mv $PWD/outdir/output_db-pass.tab $output + +rm -rf $PWD/outdir/ |