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--- trinity-software [2015/03/20 15:28] – [Usage] aorth
+++ trinity-software [2020/10/28 11:28] (current) – aorth
@@ Line 4: / Line 4: @@
 ===== Information =====
-  * Version: v2.0.3
+  * Latest Version: v2.11.0
-  * Added: February, 2014
+  * Added: March, 2015
+  * Updated: October, 2020
   * 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/v2.11.0
+$ 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/v2.6.6
+# create and change to a working directory on the compute node
+export WORKDIR=/var/scratch/$USER/$SLURM_JOBID
+mkdir -p $WORKDIR
+cd $WORKDIR
+# match CPUs to amount requested in SBATCH options!
+Trinity --seqType fq --max_memory 10G --left fish_R1.fastq --right fish_R2.fastq --CPU 8 --output trinity-fish2 --full_cleanup</code>
-**Note:** Trinity creates millions of small files -- which causes problems on the HPC storage server -- so you must direct output from these jobs to ///var/scratch// instead of your home folder.
 ===== Installation ======
 Notes from the sysadmin during installation:
-<code>$ cd ~/src
+<code>$ cd /tmp
-$ wget https://github.com/trinityrnaseq/trinityrnaseq/archive/v2.0.3.tar.gz
+$ wget https://github.com/trinityrnaseq/trinityrnaseq/releases/download/v2.11.0/trinityrnaseq-v2.11.0.FULL.tar.gz
-$ tar xf v2.0.3.tar.gz
+$ tar xf trinityrnaseq-v2.11.0.FULL.tar.gz
-$ cd trinityrnaseq-2.0.3
+$ cd trinityrnaseq-v2.11.0
-$ sudo mkdir /export/apps/trinity/v2.0.3
+$ sed -i 's/cmake/cmake3/' Chrysalis/Makefile Inchworm/Makefile
-$ sudo chown aorth /export/apps/trinity/v2.0.3
-$ cp -r * /export/apps/trinity/v2.0.3
-$ scl enable devtoolset-2 bash
 $ make
 $ make plugins
-$ sudo chown -R root:root /export/apps/trinity/v2.0.3</code>
+$ sudo yum install python36-numpy.x86_64
+$ sudo mkdir -p /export/apps/trinity/v2.11.0
+$ 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.