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shannon-software [2017/03/03 10:09] (current)
joguya created
Line 1: Line 1:
 +====== 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>​
  
shannon-software.txt · Last modified: 2017/03/03 10:09 by joguya