ILRI Research Computing

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====== Oases ======
De novo transcriptome assembler for very short reads.

===== Information =====

  * Version: 0.2.08
  * Added: May 27, 2014
  * Link: https://www.ebi.ac.uk/~zerbino/oases/

When used in conjunction with one another, Velvet and Oases __must be appropriately matched by version/release__, and also, based upon the value of **MAXKMERLENGTH** (the maximum hash length) and **CATEGORIES** (the number of short read categories), which should also be matched during respective builds.

===== Usage =====
=== Extra info ===
  * Example SLURM scripts: https://github.com/harvardinformatics/bioblog/tree/master/Trinity.Oases.Assembly

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

<code>wget https://www.ebi.ac.uk/~zerbino/velvet/velvet_1.2.10.tgz
tar zxf velvet_1.2.10.tgz
wget https://www.ebi.ac.uk/~zerbino/oases/oases_0.2.08.tgz
tar zxf oases_0.2.08.tgz
cd oases_0.2.08
scl enable devtoolset-1.1 bash
make 'VELVET_DIR=../velvet_1.2.10'
sudo mkdir -p /export/apps/oases/0.2.08/bin
sudo cp oases scripts/oases_pipeline.py /export/apps/oases/0.2.08/bin/
sudo cp OasesManual.pdf /export/apps/oases/0.2.08/</code>