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set up tscc account (epigen group) in LIMS to run pipeline

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avialee edited this page Mar 9, 2021 · 1 revision

    1. change TSCC_ACOUNT to **@tscc-login.sdsc.edu in file /home/zhc268/epigen_ucsd_django/deploy.ini
    1. create folder
    ssh **@tscc-login.sdsc.edu
    mkdir "/oasis/tscc/scratch/$(whoami)/outputs_TA/"
    mkdir "/oasis/tscc/scratch/$(whoami)/outputs/"


    ssh **@tscc-login.sdsc.edu
    ssh-keygen -t rsa
    cat .ssh/id_rsa.pub | ssh [email protected] 'cat >> .ssh/authorized_keys'
    1. Add the Miniconda installer Path and scripts Path to the .bashrc file on tscc (could add it in the script file so that users do not need this step)
    export PATH=/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.31-1.b13.el6_6.x86_64/bin:$PATH
    export PATH="$PATH:/projects/ps-epigen/software/miniconda3/bin/"
    export PATH="$PATH:/projects/ps-epigen/software/bin/"
    export PATH="$PATH:/projects/ps-epigen/software/setQC/"
    export PATH="$PATH:/projects/ps-epigen/software/.bds/"
    export _JAVA_OPTIONS="-Xms256M -Xmx728M -XX:ParallelGCThreads=1"
    export PATH="$PATH:/projects/ps-epigen/software/atac_dnase_pipelines/"
    export PATH="$PATH:/projects/ps-epigen/software/atac_dnase_pipelines/ataqc/"
    export PATH="$PATH:/projects/ps-epigen/software/atac_dnase_pipelines/utils/"
    export PATH="$PATH:/projects/ps-epigen/software/fastq_screen_v0.11.2/"
    export PICARDROOT="/projects/ps-epigen/software/miniconda3/envs/bds_atac/share/picard-1.126-4/"
    export PATH="$PATH:/projects/ps-epigen/software/setQC/utility/"
    export PATH="$PATH:/projects/ps-epigen/software/bcl2fastq/bin/"
    export PATH="$PATH:/projects/ps-epigen/software/scATAC/bin/"
    alias tree="tree  -DtlCfsh"
    PATH=$PATH:/home/opoirion/go/local/bin
    export NPY_MKL_FORCE_INTEL=true

Some conda environments need to be activated, like 'bds_atac', 'bds_atac_py3', 'aquas_chipseq', when running the pipeline. All of them are installed under folder /projects/ps-epigen/software/.

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