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w2rap

WGS (Wheat) Robust Assembly Pipeline.

Information

Usage

See versions of w2rap which are available:

$ module avail w2rap

Load one version into your environment:

$ module load w2rap/git-60781b6c

Note: there is a step-by-step walk through available on the project website: README.md. You might also want to load the modules for fastqc, BUSCO, or quast depending on the analysis you're doing.

Installation

Notes from the sysadmin during installation:

$ cd /tmp
$ git clone --recursive https://github.com/bioinfologics/w2rap.git
$ cd w2wrap
$ scl enable devtoolset-4 bash
$ cmake3 .
$ make
$ cd deps/soap_scaffolder
$ make
$ cd -
$ sudo mkdir -p /export/apps/w2rap/git-60781b6c
$ sudo chown aorth /export/apps/w2rap/git-60781b6c
$ module load python/3.6.2
$ python -m venv /export/apps/w2rap/git-60781b6c
$ . /export/apps/w2rap/git-60781b6c/bin/activate
$ pip install biopython matplotlib
$ deactivate
$ cp -v bin/dedup_fastq deps/soap_scaffolder/s_* lmp_processing SOAP_n_remapper.py /export/apps/w2rap/git-60781b6c/bin
$ sudo chown -R root:root /export/apps/w2rap/git-60781b6c
w2rap-software.txt · Last modified: 2017/10/29 15:34 by aorth