ILRI Research Computing

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====== Shannon ======

Shannon is a program for assembling transcripts from RNA-Seq data.

===== Information =====

  * Version: 0.0.2
  * Added: March, 2017
  * Link: https://sreeramkannan.github.io/Shannon/

===== Usage =====

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

Load shannon
<code>$ module load shannon/0.0.2</code>

===== Installation ======

Notes from the sysadmin during installation:

<code>
-> install metis; a dependency of shannon
$ cd /tmp
$ wget http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/metis-5.1.0.tar.gz -qO - | tar xv
$ cd metis-5.1.0
$ scl enable devtoolset-2 bash
$ sudo mkdir -p /export/apps/metis/5.1.0/
$ sudo chown joguya:joguya /export/apps/metis/5.1.0/
$ make config prefix=/export/apps/metis/5.1.0/
$ make
$ make install
$ sudo chown -R root:root /export/apps/metis/5.1.0/

-> install cvxopt; a dependency of shannon
$ cd /tmp
$ wget https://github.com/cvxopt/cvxopt/archive/1.1.9.tar.gz -qO - | tar xzv
$ cd cvxopt-1.1.9/
$ scl enable devtoolset-2 bash
$ module load python/2.7.8
# yum install suitesparse-devel
$ sudo chown -R joguya:joguya /export/apps/python/2.7.8/
$ pip install cvxopt

-> install shannon
$ cd /tmp/
$ scl enable devtoolset-3 bash
$ wget https://github.com/sreeramkannan/Shannon/archive/0.0.2.tar.gz
$ tar -xvf 0.0.2.tar.gz
$ cd Shannon-0.0.2/
$ sudo mkdir -p /export/apps/shannon/0.0.2
$ sudo cp -r . /export/apps/shannon/0.0.2
</code>