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--- trinity-software [2015/03/24 08:00] – [Installation] joguya
+++ trinity-software [2018/03/27 16:00] – aorth
@@ Line 4: / Line 4: @@
 ===== Information =====
-  * Version: v2.0.6
+  * Latest Version: v2.6.6
   * Added: March, 2015
+  * Updated: March, 2018
   * Link: https://trinityrnaseq.github.io
 ===== Usage =====
+See versions of trinity which are available:
+<code>$ module avail trinity</code>
-=== See versions of trinity which are available ===
+Load one version into your environment and run it:
-<code>module avail trinity</code>
+<code>$ module load trinity/v2.6.6
+$ Trinity</code>
-**Note:** 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:
+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
-<code>#!/bin/env bash
+  * 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 10
+#SBATCH -n 8
-module load trinity/v2.0.3
+module load trinity/v2.6.6
-module load bowtie/1.1.1
-module load samtools/1.2
-# cd to working dir just in case
+# create and change to a working directory on the compute node
-export WORKDIR=$SLURM_JOBID
+export WORKDIR=/var/scratch/$USER/$SLURM_JOBID
+mkdir -p $WORKDIR
 cd $WORKDIR
 # match CPUs to amount requested in SBATCH options!
-Trinity --seqType fq --max_memory 10G --left fish_R1.fastq --right fish_R2.fastq --CPU 10 --output trinity-fish2</code>
+Trinity --seqType fq --max_memory 10G --left fish_R1.fastq --right fish_R2.fastq --CPU 8 --output trinity-fish2 --full_cleanup</code>
 ===== Installation ======
 Notes from the sysadmin during installation:
-<code>
+<code>$ cd /tmp
-$ sudo su - provisioning
+$ wget https://github.com/trinityrnaseq/trinityrnaseq/releases/download/Trinity-v2.6.6/Trinityrnaseq-v2.6.6.wExtSampleData.tar.gz
-$ cd src
+$ tar xf Trinityrnaseq-v2.6.6.wExtSampleData.tar.gz
-$ wget "https://github.com/trinityrnaseq/trinityrnaseq/archive/v2.0.6.tar.gz" -O trinity-v2.0.6.tar.gz
+$ cd Trinityrnaseq-v2.6.6
-$ tar -xvf trinity-v2.0.6.tar.gz
+$ make
-$ cd trinityrnaseq-2.0.6/
+$ make plugins
-$ scl enable devtoolset-2 bash
+$ sudo yum install numpy
-$ CC=clang make
+$ sudo mkdir /export/apps/trinity/v2.6.6
-$ CC=clang make plugins
+$ make test_trinity
-$ sudo mkdir /export/apps/trinity/v2.0.6
+$ sudo cp -r . /export/apps/trinity/v2.6.6</code>
-$ sudo chown -R provisioning:provisioning /export/apps/trinity/v2.0.6
-$ cp -r * /export/apps/trinity/v2.0.6
+Consult the [[https://github.com/trinityrnaseq/trinityrnaseq/wiki/Installing-Trinity|installing Trinity]] guide in the documentation, although it misses some dependencies!
-$ sudo chown -R root:root /export/apps/trinity/v2.0.6
-</code>