ILRI Research Computing

User Tools

Site Tools

You are here: start » trinity-software
trinity-software

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revisionPrevious revision
Next revisionBoth sides next revision
trinity-software [2017/08/22 12:20] – aorthtrinity-software [2018/03/27 16:00] – aorth
Line 4: Line 4:
 ===== Information ===== ===== Information =====
  
-  * Latest Version: v2.4.0+  * Latest Version: v2.6.6
   * Added: March, 2015   * Added: March, 2015
-  * Updated: August, 2017+  * Updated: March, 2018
   * Link: https://trinityrnaseq.github.io   * Link: https://trinityrnaseq.github.io
  
 ===== Usage ===== ===== Usage =====
- 
 See versions of trinity which are available: See versions of trinity which are available:
- 
 <code>$ module avail trinity</code> <code>$ module avail trinity</code>
  
-**Note:** +Load one version into your environment and run it: 
-  * You should use the **−−full_cleanup** option so that Trinity can clean up after itself by removing all the intermediary files it has created except for the final Trinity.fasta results file. +<code>$ module load trinity/v2.6.6 
-  * Trinity creates millions of small files -- which causes problems on the HPC storage server -- so you must direct output from these jobs to ///var/scratch// instead of your home folder. For example:<code>#!/usr/bin/env bash+$ Trinity</code> 
 + 
 +**Notes about running Trinity:** 
 +  * Please use the **−−full_cleanup** option so that Trinity can clean up after itself by removing all the intermediary files it has created except for the final fasta results 
 +  * Trinity creates millions of small files, which is inefficient and causes problems on the HPC storage server, so you please direct the output from these jobs to a directory inside ///var/scratch// instead of your home folder. 
 +  * For example: 
 +  * <code>#!/usr/bin/env bash
 #SBATCH -p highmem #SBATCH -p highmem
 #SBATCH -J trinity #SBATCH -J trinity
 #SBATCH -n 8 #SBATCH -n 8
  
-module load trinity/v2.4.0+module load trinity/v2.6.6
  
 # create and change to a working directory on the compute node # create and change to a working directory on the compute node
Line 36: Line 40:
  
 <code>$ cd /tmp <code>$ cd /tmp
-$ wget https://github.com/trinityrnaseq/trinityrnaseq/archive/Trinity-v2.4.0.zip +$ wget https://github.com/trinityrnaseq/trinityrnaseq/releases/download/Trinity-v2.6.6/Trinityrnaseq-v2.6.6.wExtSampleData.tar.gz 
-$ unzip Trinity-v2.4.0.zip +$ tar xf Trinityrnaseq-v2.6.6.wExtSampleData.tar.gz 
-$ cd trinityrnaseq-Trinity-v2.4.0 +$ cd Trinityrnaseq-v2.6.6
-$ scl enable devtoolset-4 bash+
 $ make $ make
 $ make plugins $ make plugins
-$ sudo mkdir /export/apps/trinity/v2.4.0+$ sudo yum install numpy 
 +$ sudo mkdir /export/apps/trinity/v2.6.6
 $ make test_trinity $ make test_trinity
-$ sudo cp -r . /export/apps/trinity/v2.4.0</code>+$ sudo cp -r . /export/apps/trinity/v2.6.6</code> 
 + 
 +Consult the [[https://github.com/trinityrnaseq/trinityrnaseq/wiki/Installing-Trinity|installing Trinity]] guide in the documentation, although it misses some dependencies!
trinity-software.txt · Last modified: 2020/10/28 11:28 by aorth