Differences

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

--- trinity-software [2017/08/22 12:20] – aorth
+++ trinity-software [2020/10/28 11:28] (current) – aorth
@@ Line 4: / Line 4: @@
 ===== Information =====
-  * Latest Version: v2.4.0
+  * Latest Version: v2.11.0
   * Added: March, 2015
-  * Updated: August, 2017
+  * Updated: October, 2020
   * Link: https://trinityrnaseq.github.io
 ===== Usage =====
 See versions of trinity which are available:
 <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/v2.11.0
-  * 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 -J trinity
 #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
@@ Line 36: / Line 40: @@
 <code>$ cd /tmp
-$ wget https://github.com/trinityrnaseq/trinityrnaseq/archive/Trinity-v2.4.0.zip
+$ wget https://github.com/trinityrnaseq/trinityrnaseq/releases/download/v2.11.0/trinityrnaseq-v2.11.0.FULL.tar.gz
-$ unzip Trinity-v2.4.0.zip
+$ tar xf trinityrnaseq-v2.11.0.FULL.tar.gz
-$ cd trinityrnaseq-Trinity-v2.4.0
+$ cd trinityrnaseq-v2.11.0
-$ scl enable devtoolset-4 bash
+$ sed -i 's/cmake/cmake3/' Chrysalis/Makefile Inchworm/Makefile
 $ make
 $ make plugins
-$ sudo mkdir /export/apps/trinity/v2.4.0
+$ sudo yum install python36-numpy.x86_64
-$ make test_trinity
+$ sudo mkdir -p /export/apps/trinity/v2.11.0
-$ sudo cp -r . /export/apps/trinity/v2.4.0</code>
+$ sudo cp -r . /export/apps/trinity/v2.11.0
+$ export TRINITY_HOME=/export/apps/trinity/v2.11.0
+$ module load samtools/1.9 salmon/1.3.0 bowtie2/2.3.4.1 jellyfish/2.3.0
+$ cd sample_data/test_Trinity_Assembly
+$ ./runMe.sh</code>
+Consult the [[https://github.com/trinityrnaseq/trinityrnaseq/wiki/Installing-Trinity|installing Trinity]] guide in the documentation.