ILRI Research Computing

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====== w2rap ======
WGS (Wheat) Robust Assembly Pipeline.

===== Information =====

  * Version: git-60781b6c
  * Added: October, 2017
  * Link: https://github.com/bioinfologics/w2rap
===== Usage =====

See versions of w2rap which are available:
<code>$ module avail w2rap</code>

Load one version into your environment:
<code>$ module load w2rap/git-60781b6c</code>

Note: there is a step-by-step walk through available on the project website: [[https://github.com/bioinfologics/w2rap/blob/master/README.md|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:

<code>$ 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</code>