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trinity-software [2015/03/20 15:32] – [Usage] aorthtrinity-software [2017/08/22 12:20] – aorth
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 ===== Information ===== ===== Information =====
  
-  * Version: v2.0.3 +  * Latest Version: v2.4.0 
-  * Added: February, 2014+  * Added: March, 2015 
 +  * Updated: August, 2017
   * Link: https://trinityrnaseq.github.io   * Link: https://trinityrnaseq.github.io
  
 ===== Usage ===== ===== Usage =====
  
-=== See versions of trinity which are available === +See versions of trinity which are available:
-<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>$ module avail trinity</code>
  
-<code>#!/bin/env bash+**Note:** 
 +  * 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. 
 +  * 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
 #SBATCH -p highmem #SBATCH -p highmem
 #SBATCH -J trinity #SBATCH -J trinity
-#SBATCH -n 10+#SBATCH -n 8
  
-module load trinity/v2.0.3 +module load trinity/v2.4.0
-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 cd $WORKDIR
  
 # match CPUs to amount requested in SBATCH options! # 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 ====== ===== Installation ======
 Notes from the sysadmin during 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/Trinity-v2.4.0.zip 
-$ tar xf v2.0.3.tar.gz +$ unzip Trinity-v2.4.0.zip 
-$ cd trinityrnaseq-2.0.3 +$ cd trinityrnaseq-Trinity-v2.4.0 
-$ sudo mkdir /export/apps/trinity/v2.0.3 +$ scl enable devtoolset-4 bash
-$ sudo chown aorth /export/apps/trinity/v2.0.3 +
-$ cp -r * /export/apps/trinity/v2.0.3 +
-$ scl enable devtoolset-2 bash+
 $ make $ make
 $ make plugins $ make plugins
-$ sudo chown -R root:root /export/apps/trinity/v2.0.3</code>+$ sudo mkdir /export/apps/trinity/v2.4.0 
 +$ make test_trinity 
 +$ sudo cp -r . /export/apps/trinity/v2.4.0</code>
trinity-software.txt · Last modified: 2020/10/28 11:28 by aorth