update tests

sut:

  build: .

  command: run_tests.sh

  command: bash run_tests.sh

#!/bin/bash

#$ -N cellranger_NPO1

#$ -q bigmem.q

#$ -o cellranger_NP01.out

#$ -e cellranger_NP01_error.out

#$ -cwd

#create virtual directory of modified files

if [ ! -d cellranger ]

    then

    mkdir -p cellranger

    fi

for file in `ls *R2*.fastq | cut -d"_" -f1-3`

    do

    if [ ! -f cellranger/${file}_R1_001.fastq ]

        then

        #ln -s ../${file}_cellranger_R1_001.fastq cellranger/${file}_R1_001.fastq

        ln -s ../${file}_cellranger_R1_001.fastq cellranger/${file}_R1_001.fastq

        fi

    if [ ! -f cellranger/${file}_R2_001.fastq ]

        then

        ln -s ../${file}_R2_001.fastq cellranger/${file}_R2_001.fastq

        fi

    done

export PATH=/home/tom/local/bin/cellranger-2.1.0:$PATH

date

start=`date +%s`

cellranger count --id="test_AtRTD2" \

                 --fastqs="cellranger" \

                 --sample="NP01" \

                 --lanes="1,2" \

                 --r1-length="26" \

                 --chemistry="threeprime" \

                 --transcriptome="/home/tom/reference/cellranger/AtRTDv2/" 

#                 --noexit \

#                 --nopreflight

#                 --force-cells="2500" \

end=`date +%s`

date

runtime=$((end-start))

#edit html output

sed -i "s/test_AtRTD2/Arabidopsis \(NP01\)/g" test_AtRTD2/outs/web_summary.html

sed -i "1621s/.*/  <td><i>Arabidopsis thaliana<\/i> (NP01)<\/td>/" test_AtRTD2/outs/web_summary.html

#!/bin/bash

# run tests in home directory (writeable)

cd ~