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CTAT mutations installation

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Brian Haas edited this page Sep 10, 2023 · 20 revisions

Installation:

CTAT Mutations installation involves a combination of software and data resources leveraged by the pipeline. Each are described below.

Software Installation

Recommended - Docker or Singularity: If you use Docker or Singularity, we provide images that come with everything you need!

Otherwise, you can download and install the software and various dependencies.

CTAT-mutations Genome Lib Installation

Step 1: CTAT Genome lib setup

The CTAT-mutation lib integrates with the standard CTAT genome lib that's leveraged as part of the Trinity CTAT project. Instructions below describe how to set up your CTAT genome lib and integrate the mutation lib. It's pretty easy.

Trinity CTAT supports both human genome builds hg19/37 and hg38, so you can choose whichever version you prefer to operate from, or separately install both so you have flexibility to use either.

Download your selected plug-n-play CTAT genome lib from the Trinity CTAT Data Repository.

Note, if you already have a CTAT genome lib installed for use with other Trinity CTAT project utilities, feel free to use the genome lib you already have.

Step 2: Install the CTAT Mutation Lib Supplement

Depending on which CTAT genome lib you installed (hg19/37 or hg38), download the matching CTAT Mutation Lib Supplement.

Place the 'mutation lib tar.gz' file into the CTAT genome lib build directory (typically named 'ctat_genome_lib_build_dir/'), and unpack it:

    ie.    tar xvf mutation_lib_supplement.tar.gz

Step 3: Execute the mutation lib integration utility.

Run the CTAT mutation lib integration utility like so.

If you installed ctat_mutations directly (and aren't using Docker or Singularity), your command would be:

    python ctat-mutations/mutation_lib_prep/ctat-mutation-lib-integration.py \
        --genome_lib_dir /path/to/your/ctat_genome_lib_build_dir

Alternatively, if you're using Docker, your command is:

    docker run --rm -v /path/to/your/ctat_genome_lib_build_dir:/ctat_genome_lib_build_dir \
        trinityctat/ctat_mutations \
       /usr/local/src/ctat-mutations/mutation_lib_prep/ctat-mutation-lib-integration.py \
       --genome_lib_dir /ctat_genome_lib_build_dir

Alternatively, if you're running Singularity, your command is:

   singularity exec -e -B /path/to/your/ctat_genome_lib_build_dir \
      ctat-mutations.simg \
      /usr/local/src/ctat-mutations/mutation_lib_prep/ctat-mutation-lib-integration.py \
      --genome_lib_dir /path/to/your/ctat_genome_lib_build_dir

Step 4: Install Open-CRAVAT and related annotation resources

Open-CRAVAT is easily installed using pip.

If using Singularity or Docker, it's already installed, so don't run this step to install the Open-Cravat software. See below for installing the open-cravat data library.

pip install requests open-cravat==2.0.1

Next, install the open-cravat resources needed by using the Open-CRAVAT 'oc' utility. This will populate a 'cravat' subdirectory of your ctat_mutation_lib directory:

this is needed even if you're using Docker or Singularity, as it's part of configuring your CTAT genome lib.

Visit our cravat data library directory and download the tar.bz2 file corresponding to your genome lib (GRCh38 or 37).

Place this tar.bz2 file in your ctat genome library and unpack it

# from within your ctat genome library directory:

tar xvf cravat.tar.bz2 # use the name of the tar.bz2 file you downloaded

Congratulations! Your CTAT genome lib is now fully configured for use with the ctat-mutations pipeline.

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