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w2rap-software [2017/10/29 15:34] (current)
aorth created
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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>​
w2rap-software.txt · Last modified: 2017/10/29 15:34 by aorth