Offer a Successful singularity def file

[fish2022Jul]

Thanks to the authors for your hard working on this app!!! but there is lot of errors before I can use it with singularity. I spent several days on setting it up. this def file contains install root, change permition within /app/clinsv/bigWigTools/ and add font tcss1000

Bootstrap: docker
From: mrbradley2/clinsv:v1.1-dev

%post
    apt-get update
    apt install -y  git ca-certificates make  unzip curl wget gcc

    wget https://root.cern/download/root_v6.26.14.Linux-ubuntu20-x86_64-gcc9.4.tar.gz
    tar -xzvf root_v6.26.14.Linux-ubuntu20-x86_64-gcc9.4.tar.gz
    source root/bin/thisroot.sh
    chmod 755 /app/clinsv/bigWigTools/wigToBigWig
    chmod 755 /app/clinsv/bigWigTools/bigWigToWig
    cd /usr/share/texmf/fonts/tfm/public/tex-gyre
    wget https://mirrors.ctan.org/fonts/ec/tfm/tcss1000.tfm
    mktexlsr

%environment
   export LC_ALL=C
   PATH=/app/clinsv/bin/:$PATH

===================================

And then run it with following bash ###############

#the sample dir contains bam file NA12878.grch38.subsampled.bam
cd /data/$USER/test_data/sample
refdata_path=/usr/local/apps/clinsv/ref_hg38/clinsv/refdata-b38
input_path=$PWD
project_folder=$PWD/test_run

singularity run --bind $refdata_path:/app/ref-data/refdata-b38 --bind $project_folder:/app/project_folder \
        --bind $input_path:/app/input /data/$USER/test_data/sample/sif/1.1.sif \
        /app/clinsv/bin/clinsv \
        -r all \
        -p /app/project_folder/ \
        -i "/app/input/*.bam" \
        -ref /app/ref-data/refdata-b38

########################

Finally, thanks to NIH HPC Biowulf