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Copy pathsnake.cmd.generate.snake.sh
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snake.cmd.generate.snake.sh
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#!/usr/bin/env bash
set –euo pipefail
if [[ -e .snakemake ]]; then find .snakemake/ -delete ; fi
if [[ -e logs ]]; then find logs -delete ; fi
snakemake -q -j 200 -k -s ./snake.cmd.generate.snake --cluster-config cluster.json --cluster "qsub -j y -o logs -pe smp {cluster.smp} -l h_vmem={cluster.h_vmem}"
#--------------------------------------------------
# for queryDir in `ls -d batsGenome/eonSpe`
#--------------------------------------------------
#--------------------------------------------------
# for queryDir in `ls -d batsGenome/[[:lower:]]*[[:upper:]]*`
# do
# queryID="`basename $queryDir`2"
# nibQueryDir="$queryDir/$queryID.nib2"
# for targetDir in `ls -d batsGenome/pteAle`
# do
# targetID=`basename $targetDir`
# if [ $targetID != "hg38" ]; then
# targetID=$targetID"2"
# fi
# if [[ $queryID == $targetID || $queryDone == *"$targetID"* || $queryID == "eidHel2" || $queryID == "eonSpe2" ]]; then
# continue
# fi
# lavQueryDir="$queryDir/$queryID.$targetID.lav"
# pslQueryDir="$queryDir/$queryID.$targetID.psl"
# chainQueryDir="$queryDir/$queryID.$targetID.chain"
# nibTargetDir="$targetDir/$targetID.nib2"
# snakeDir="snake.$queryID.$targetID"
# for i in `find $nibQueryDir/ -name *.nib`
# do
# queryChr=`basename $i .nib`
# if [[ ! -e $snakeDir/$queryChr.snake.done ]]; then
# echo "find $lavQueryDir/$queryChr -delete" >> $snakeDir/$queryChr.snake.cmd
# echo "find $pslQueryDir/$queryChr -delete" >> $snakeDir/$queryChr.snake.cmd
# echo "find $chainQueryDir/$queryChr -delete" >> $snakeDir/$queryChr.snake.cmd
# touch $snakeDir/$queryChr.snake.done
# fi
# done
# done
# done
#--------------------------------------------------