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--- trinity-software [2015/02/12 11:37] – created aorth
+++ trinity-software [2015/07/31 11:59] – 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
 ===== Usage =====
-=== See versions of trinity which are available ===
+See versions of trinity which are available:
-<code>module avail trinity</code>
+<code>$module avail trinity</code>
+**Note:**
+  * You should always use the **--full_cleanup** option so that Trinity can clean up after itself by removing all the intermediary files it has created except for the final Trinity.fasta results file.
+  * Trinity creates millions of small files -- which causes problems on the HPC storage server -- so you must direct output from these jobs to ///var/scratch// instead of your home folder. For example:<code>#!/bin/env bash
+#SBATCH -p highmem
+#SBATCH -J trinity
+#SBATCH -n 8
+module load trinity/v2.0.6
+module load bowtie/1.1.1
+module load samtools/1.2
+# cd to working dir just in case
+export WORKDIR=/var/scratch/$USER/$SLURM_JOBID
+mkdir -p $WORKDIR
+cd $WORKDIR
+# match CPUs to amount requested in SBATCH options!
+Trinity --seqType fq --max_memory 10G --left fish_R1.fastq --right fish_R2.fastq --CPU 8 --output trinity-fish2</code>
 ===== Installation ======
 Notes from the sysadmin during installation:
-<code>$ cd ~/src
+<code>$ cd /tmp
-$ wget https://github.com/trinityrnaseq/trinityrnaseq/archive/v2.0.3.tar.gz
+$ wget "https://github.com/trinityrnaseq/trinityrnaseq/archive/v2.0.6.tar.gz" -O trinity-v2.0.6.tar.gz
-$ tar xf v2.0.3.tar.gz
+$ tar -xvf trinity-v2.0.6.tar.gz
-$ cd trinityrnaseq-2.0.3
+$ cd trinityrnaseq-2.0.6/
-$ sudo mkdir /export/apps/trinity/v2.0.3
-$ sudo chown aorth /export/apps/trinity/v2.0.3
-$ 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
+$ cp -r * /export/apps/trinity/v2.0.6
+$ sudo chown -R root:root /export/apps/trinity/v2.0.6</code>