ILRI Research Computing

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====== ngs-tools ======

===== Information =====

  * Version: 3.0.0
  * Added: March, 2022
  * Link: https://github.com/ncbi/ngs-tools

===== Usage =====

See versions which are available:
<code>$ module avail ngs-tools</code>

Load one version into your environment and run it:

<code>$ module load ngs-tools/3.0.0
$ sra-search
$ compute-coverage</code>

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

<code>$ cd /tmp
$ git clone https://github.com/ncbi/ngs-tools.git -b 3.0.0
$ cd ngs-tools
$ scl enable devtoolset-7 bash
$ ./configure --prefix=/export/apps/ngs-tools/3.0.0 --with-ncbi-vdb-sources=/export/apps/ncbi-vdb/3.0.0 --with-ncbi-vdb-build=/export/apps/ncbi-vdb/3.0.0 --with-sra-tools-build=/export/apps/sra-tools/3.0.0 --build-prefix=/tmp/foo
$ make # errors the first time...?
$ make
$ sudo mkdir -p /export/apps/ngs-tools/3.0.0
$ sudo chown aorth /export/apps/ngs-tools/3.0.0
$ make install
$ sudo chown -R root:root /export/apps/ngs-tools/3.0.0</code>

Requires ncbi-vdb and sra-tools also (compiled separately into /export/apps).