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--- trinity-software [2015/02/12 11:37] – created aorth
+++ trinity-software [2015/03/24 08:00] – [Installation] joguya
@@ Line 4: / Line 4: @@
 ===== Information =====
-  * Version: v2.0.3
+  * Version: v2.0.6
-  * Added: February, 2013
+  * Added: March, 2015
   * Link: https://trinityrnaseq.github.io
@@ Line 13: / Line 13: @@
 <code>module avail 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:
+<code>#!/bin/env bash
+#SBATCH -p highmem
+#SBATCH -J trinity
+#SBATCH -n 10
+module load trinity/v2.0.3
+module load bowtie/1.1.1
+module load samtools/1.2
+# cd to working dir just in case
+export WORKDIR=$SLURM_JOBID
+cd $WORKDIR
+# match CPUs to amount requested in SBATCH options!
+Trinity --seqType fq --max_memory 10G --left fish_R1.fastq --right fish_R2.fastq --CPU 10 --output trinity-fish2</code>
 ===== Installation ======
 Notes from the sysadmin during installation:
-<code>$ cd ~/src
+<code>
-$ wget https://github.com/trinityrnaseq/trinityrnaseq/archive/v2.0.3.tar.gz
+$ sudo su - provisioning
-$ tar xf v2.0.3.tar.gz
+$ cd src
-$ cd trinityrnaseq-2.0.3
+$ wget "https://github.com/trinityrnaseq/trinityrnaseq/archive/v2.0.6.tar.gz" -O trinity-v2.0.6.tar.gz
-$ sudo mkdir /export/apps/trinity/v2.0.3
+$ tar -xvf trinity-v2.0.6.tar.gz
-$ sudo chown aorth /export/apps/trinity/v2.0.3
+$ cd trinityrnaseq-2.0.6/
-$ cp -r * /export/apps/trinity/v2.0.3
 $ scl enable devtoolset-2 bash
-$ make
+$ CC=clang make
-$ make plugins
+$ CC=clang make plugins
-$ sudo chown -R root:root /export/apps/trinity/v2.0.3</code>
+$ sudo mkdir /export/apps/trinity/v2.0.6
+$ sudo chown -R provisioning:provisioning /export/apps/trinity/v2.0.6
+$ cp -r * /export/apps/trinity/v2.0.6
+$ sudo chown -R root:root /export/apps/trinity/v2.0.6
+</code>