clusterflow-0.5_install

#!/usr/bin/bash -i

###############################################
# Installing OMA standalone
#
# by Javier Herrero, 2016 
#

APPNAME=${APPNAME:-clusterflow}
VERSION=${VERSION:-0.5}
INSTALL_PREFIX=${INSTALL_PREFIX:-/shared/ucl/depts/cancer/apps/$APPNAME/}
MD5=${MD5:-d38a7ee9f7be1f19eca41c0971be6f3b}
SHA1=${SHA1:-REPLACE}
SRC_ARCHIVE=${SRC_ARCHIVE:-https://github.com/ewels/clusterflow/archive/v${VERSION}.tar.gz}

set -e

module load perl/5.22.0

export PATH=$INSTALL_PREFIX/bin:$PATH

mkdir -p $INSTALL_PREFIX

cd $INSTALL_PREFIX

wget -N $SRC_ARCHIVE

MD5SUM=`md5sum v${VERSION}.tar.gz | awk '{print $1}'`

if [ "$MD5SUM" == "$MD5" ]
then
    rm -rf ${VERSION}
    tar -zxf v${VERSION}.tar.gz
    mv ClusterFlow-${VERSION} ${VERSION}
    cd ${VERSION}
    cp clusterflow.config.example clusterflow.config

    sed -e 's/@max_time.*/@max_time\t48:00:00/' -i clusterflow.config
    sed -e 's/\/\* @cluster_environment.*/@cluster_environment\tGRIDEngine/' -i clusterflow.config
    sed -e 's/\/\* @custom_job_submit_command.*/@custom_job_submit_command echo "{{command}}" | qsub -b n -cwd -V -S \/bin\/bash -pe smp {{cores}} {{qname}} -l h_rt={{time}} -l mem={{mem}} -o {{outfn}} -j y -N {{job_id}} {{notifications}}/' -i clusterflow.config
    sed -e 's/\/\* @environment_module_alias <requested> <replacement> \*\//\/\* @environment_module_alias <requested> <replacement> \*\/\n@environment_module_alias cutadapt python3\/recommended/' -i clusterflow.config

    sed -e 's/2-00:00:00/48:00:00/' -i cf
    sed -e "s/'12:00'/'0:12:00'/" -i cf
    
    cat > source/CF/Helpers.pm.patch <<EOF
678,679d677
<     my \$days = int(\$minutes / (24 * 60));
<     \$minutes -= \$days * 24 * 60;
688,694c686
<     if(\$days > 0){
<         return "\$days-\$hours:\$minutes";
<     } elsif(\$hours > 0){
<         return "\$hours:\$minutes:00";
<     } else {
<         return "\$minutes";
<     }
---
>     return "\$hours:\$minutes:00";
EOF

    patch source/CF/Helpers.pm < source/CF/Helpers.pm.patch

    cat > cf.patch <<EOF
742c742,744
< unless(\$cl_dryrun){
---
> if(\$cl_dryrun){
>     *SUBMIT = *STDOUT;
> } else {
EOF

    patch cf < cf.patch

    if [[ -e /scratch/scratch/regmr01/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa ]]
    then
        perl -le 'print join("\t", "\@reference", "fasta", "GRCh38", "/scratch/scratch/regmr01/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/", "Human", "GRCh38")' >> genomes.d/GRCh38.config
    fi
    if [[ -e /scratch/scratch/regmr01/Homo_sapiens/NCBI/GRCh38/Sequence/BWAIndex/genome.fa ]]
    then
        perl -le 'print join("\t", "\@reference", "bwa", "GRCh38", "/scratch/scratch/regmr01/Homo_sapiens/NCBI/GRCh38/Sequence/BWAIndex/genome.fa", "Human", "GRCh38")' >> genomes.d/GRCh38.config
    fi
    if [[ -e /scratch/scratch/regmr01/Homo_sapiens/NCBI/GRCh38/Sequence/Bowtie2Index/genome.fa ]]
    then
        perl -le 'print join("\t", "\@reference", "bowtie2", "GRCh38", "/scratch/scratch/regmr01/Homo_sapiens/NCBI/GRCh38/Sequence/Bowtie2Index/genome", "Human", "GRCh38")' >> genomes.d/GRCh38.config
    fi
    if [[ -e /scratch/scratch/regmr01/Homo_sapiens/NCBI/GRCh38/Annotation/Archives/archive-2015-08-11-09-31-31/Genes.gencode/genes.gtf ]]
    then
        perl -le 'print join("\t", "\@reference", "gtf", "GRCh38", "/scratch/scratch/regmr01/Homo_sapiens/NCBI/GRCh38/Annotation/Archives/archive-2015-08-11-09-31-31/Genes.gencode/genes.gtf", "Human", "GRCh38")' >> genomes.d/GRCh38.config
    fi
    
    if [[ -e /scratch/scratch/regmr01/Mus_musculus/NCBI/GRCm38/Sequence/WholeGenomeFasta/genome.fa ]]
    then
        perl -le 'print join("\t", "\@reference", "fasta", "GRCm38", "/scratch/scratch/regmr01/Mus_musculus/NCBI/GRCm38/Sequence/WholeGenomeFasta/", "Mouse", "GRCm38")' >> genomes.d/GRCm38.config
    fi
    if [[ -e /scratch/scratch/regmr01/Mus_musculus/NCBI/GRCm38/Sequence/BWAIndex/version0.6.0/genome.fa.bwt ]]
    then
        perl -le 'print join("\t", "\@reference", "bwa", "GRCm38", "/scratch/scratch/regmr01/Mus_musculus/NCBI/GRCm38/Sequence/BWAIndex/version0.6.0/genome.fa", "Mouse", "GRCm38")' >> genomes.d/GRCm38.config
    fi
    if [[ -e /scratch/scratch/regmr01/Mus_musculus/NCBI/GRCm38/Sequence/Bowtie2Index/genome.1.bt2 ]]
    then
        perl -le 'print join("\t", "\@reference", "bowtie2", "GRCm38", "/scratch/scratch/regmr01/Mus_musculus/NCBI/GRCm38/Sequence/Bowtie2Index/genome", "Mouse", "GRCm38")' >> genomes.d/GRCm38.config
    fi
    if [[ -e /scratch/scratch/regmr01/Homo_sapiens/NCBI/GRCh38/Annotation/Archives/archive-2015-08-11-09-31-31/Genes.gencode/genes.gtf ]]
    then
        perl -le 'print join("\t", "\@reference", "gtf", "GRCm38", "/scratch/scratch/regmr01/Homo_sapiens/NCBI/GRCh38/Annotation/Archives/archive-2015-08-11-09-31-31/Genes.gencode/genes.gtf", "Mouse", "GRCm38")' >> genomes.d/GRCm38.config
    fi
    
else
    echo "Hash mismatch."
    echo "Expected: $MD5"
    echo "Got: $MD5SUM"
    exit
fi