Commit 45bba403 authored by TomKellyGenetics's avatar TomKellyGenetics
Browse files

update syntax for renaming files automatically

parent f9c79676

launch_universc.sh

+2 −2
Original line number Diff line number Diff line
@@ -1445,9 +1445,9 @@ for key in ${keys[@]}; do 
                    echo "  renaming $read ..."

                fi

                k=$((${j} + 1))

                rename -f "s/_L([0-9][0123456789][0123456789])/_S${k}_L\$1/" ${read}*

                rename -f "s/_L\([0123456789][0123456789][0123456789]\)/_S${k}_L\1/" ${read}*

                #update file variable

                read=`echo $read | perl -pn -e "s/_L([0-9][0123456789][0123456789])/_S${k}_L\$1/g"`

                read=`echo $read | perl -pn -e "s/_L\([0123456789][0123456789][0123456789]\)/_S${k}_L\1/g"`

                list[$j]=$read

            ;;

        esac

test/run_tests_icell8_local.sh

+2 −2
Original line number Diff line number Diff line
@@ -68,7 +68,7 @@ bash launch_universc.sh --id "test-icell8-72618_KU812-2-lanes" --technology "iCe 
 --read1 "test/shared/icell8-test/72618_KU812_L001_R1_001.fastq" "test/shared/icell8-test/72618_KU812_L002_R1_001.fastq" \

 --read2 "test/shared/icell8-test/72618_KU812_L001_R2_001.fastq" "test/shared/icell8-test/72618_KU812_L002_R2_001.fastq" \

 --barcodefile "test/shared/icell8-test/WellList.txt" \

 --per-cell-data --jobmode "local" --localcores 2 --localmem 4

 --per-cell-data --jobmode "local" --localcores 2 --localmem 4 --verbose



if [ -f test/shared/icell8-test/72618_KU812_S1_L001_R1_001.fastq ]; then

    rename "s/_S1_L001/_L001/" test/shared/icell8-test/72618_KU812_S1_L001_R1_001.fastq*
@@ -93,7 +93,7 @@ bash launch_universc.sh --id "test-icell8-72618_KU812-1-lane" --technology "iCel 
 --read1 "test/shared/icell8-test/72618_KU812_L001_R1_001.fastq" \

 --read2 "test/shared/icell8-test/72618_KU812_L001_R2_001.fastq" \

 --barcodefile "test/shared/icell8-test/WellList.txt" \

 --per-cell-data --jobmode "local" --localcores 2 --localmem 4

 --per-cell-data --jobmode "local" --localcores 2 --localmem 4 --verbose



if [ -f test/shared/icell8-test/72618_KU812_S1_L001_R1_001.fastq ]; then

    rename "s/_S1_L001/_L001/" test/shared/icell8-test/72618_KU812_S1_L001_R1_001.fastq*

test/run_tests_smartseq3_local_diyspike.sh

deleted100755 → 0
+0 −60
Original line number Diff line number Diff line 


#!/bin/bash

bash ~/.bashrc



# run tests in universc directory (parent of test directory)

cd $(dirname ${BASH_SOURCE[0]})/..

pwd

##git pull --ff-only origin $(git branch --show-current) 



# used to export to PATH for testing on SGE server

export PATH=${HOME}/local/bin/cellranger-3.0.2:$PATH



cellrangerversion=`cellranger count --version | head -n 2 | tail -n 1 | cut -f2 -d'(' | cut -f1 -d')'`

cellrangerpath=`which cellranger`



# set up cellranger reference

if [[ ! -f test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/SA ]] && [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/3.0.0/star/SA ]]; then

    rsync $(dirname $cellrangerpath)/cellranger-tiny-ref/3.0.0/star/SA test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/SA

fi

if [[ ! -f test/cellranger_reference/cellranger-tiny-ref/1.2.0/star/SA ]] && [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.0/star/SA ]]; then

    rsync $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.0/star/SA test/cellranger_reference/cellranger-tiny-ref/1.2.0/star/SA

fi



# compress all input files

if [[ -f test/shared/smartseq3-test/Smartseq3_diySpike_S1_L001_S1_R1_001.fastq ]]; then

echo    gzip test/shared/smartseq3-test/Smartseq3_diySpike_S1_L00?_S1_[IR][12]_001.fastq.gz

fi



#rename "s/Smartseq3.diySpike./Smartseq3_diySpike_/g"  test/shared/smartseq3-test/Smartseq3.diySpike.[IR][12].fastq

#rename "s/Smartseq3.diySpike./Smartseq3_diySpike_/g"  test/shared/smartseq3-test/Smartseq3.diySpike.L001.[IR][12].fastq



while [[ ! -f /home/tom/repos/universc/test-10x-hek293t/outs/metrics_summary.csv  ]]; do

    echo "wait ..."

    sleep 60

done



# test manual setup

bash launch_universc.sh -t "smartseq3" --setup  --barcodefile "whitelists/test_bcs_smartseq3_full.txt"



if [[ -d input4cellranger_test-smartseq3-diyspike-hg38 ]]; then

    rm -rf input4cellranger_test-smartseq3-diyspike-hg38

fi

if [[ -d test-smartseq3-diyspike-hg38 ]]; then

    rm -rf test-smartseq3-diyspike-hg38

fi



if [[ ! -f whitelists/SmartSeq3_test_barcodes.txt ]]; then

    gunzip -k whitelists/SmartSeq3_test_barcodes.txt.gz

fi



 # call on smartseq3 with files

bash launch_universc.sh --id "test-smartseq3-diyspike-hg38" --technology "smartseq3" \

 --chemistry "SC5P-PE" \

 --reference "~/reference/cellranger/refdata-cellranger-GRCh38-3.0.0" \

 --barcodefile "whitelists/test_bcs_smartseq3_full.txt" \

 --read1 "test/shared/smartseq3-test/Smartseq3_diySpike_S1_L001_R1_001.fastq" \

 --read2 "test/shared/smartseq3-test/Smartseq3_diySpike_S1_L001_R2_001.fastq" \

 --index1 "test/shared/smartseq3-test/Smartseq3_diySpike_S1_L001_I1_001.fastq" \

 --index2 "test/shared/smartseq3-test/Smartseq3_diySpike_S1_L001_I2_001.fastq" \

 --per-cell-data --jobmode "local" --verbose #--as-is # "local" --localcores 1

test/shared/dropseq-test/SRR1873277_Sample1_R1.fastq.gz

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test/shared/dropseq-test/SRR1873277_Sample1_R2.fastq.gz

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