ILRI Research Computing

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====== genomeworks ======
SDK for GPU accelerated genome assembly and analysis.

===== Information =====

  * Version: git-baab5668
  * Added: September, 2021
  * Link: https://github.com/clara-parabricks/GenomeWorks

===== Usage =====

See versions of genomeworks that are available:
<code>$ module avail genomeworks</code>

Load one version into your environment and run it:
<code>$ module load genomeworks/git-baab5668
$ cudamapper
$ cudapoa</code>

**Note:** genomeworks only works on nodes that have an Nvidia GPU (currently only compute06).

===== Installation ======
Notes from the sysadmin during installation.

<code>$ cd /tmp
$ git clone --recursive -b dev https://github.com/clara-parabricks/GenomeWorks.git
$ cd GenomeWorks
$ mkdir build && cd build
$ scl enable devtoolset-7 bash
$ module load python/3.8
$ cmake3 .. -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/export/apps/genomeworks/git-baab5668 -Dgw_cuda_gen_all_arch=OFF -Dgw_build_htslib=ON
$ make
$ sudo mkdir -p /export/apps/genomeworks/git-baab5668
$ sudo chown aorth /export/apps/genomeworks/git-baab5668
$ make install
$ sudo chown -R root:root /export/apps/genomeworks/git-baab5668</code>

I compiled from the ''dev'' branch because the latest release tag (v2021.02.2) has build issues in our environment.