update tests

#! /bin/bash

bash launch_universc.sh --id "test-in-v2" --technology "indrop2" \

 --reference "test/cellranger_reference/cellranger-tiny-ref/3.0.0" \

 --file "/home/tom/datasets/indropsv2_public_data/lib1_L001" \

 "/home/tom/datasets/indropsv2_public_data/lib1_L002" "/home/tom/datasets/indropsv2_public_data/lib1_L003" "/home/tom/datasets/indropsv2_public_data/lib1_L004" \

 --per-cell-data --jobmode "local" --localcores 8

bash launch_universc.sh --id "test-in-v1" --technology "indrop1" \

 --reference "test/cellranger_reference/cellranger-tiny-ref/3.0.0" \

 --file "/home/tom/datasets/indropsv1_public_data/sample_S1_L001" \

 --per-cell-data --jobmode "local" --localcores 8

rename  "s/S1_L001/L001/" /home/tom/datasets/indropsv2_public_data/sample*fastq

rename  "s/S2_L002/L002/" /home/tom/datasets/indropsv2_public_data/sample*fastq

rename  "s/S3_L003/L003/" /home/tom/datasets/indropsv2_public_data/sample*fastq

rename  "s/S4_L004/L004/" /home/tom/datasets/indropsv2_public_data/sample*fastq

#!/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