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trinity-software [2015/07/31 12:00]
joguya [Usage]
trinity-software [2018/03/27 16:00]
aorth
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 ===== Information ===== ===== Information =====
  
-  * Version: v2.0.6+  * Latest Version: v2.6.6
   * Added: March, 2015   * Added: March, 2015
 +  * Updated: March, 2018
   * 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>
  
-<code>$module avail trinity</code>+Load one version into your environment and run it: 
 +<code>$ module load trinity/v2.6.6 
 +$ Trinity</code>
  
-**Note:** +Notes about running Trinity
-  * 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. +  * 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 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+  * Trinity creates millions of small fileswhich is inefficient and causes problems on the HPC storage serverso 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 -p highmem
 #SBATCH -J trinity #SBATCH -J trinity
 #SBATCH -n 8 #SBATCH -n 8
  
-module load trinity/v2.0.6 +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 working directory on the compute node
 export WORKDIR=/var/scratch/$USER/$SLURM_JOBID export WORKDIR=/var/scratch/$USER/$SLURM_JOBID
 mkdir -p $WORKDIR mkdir -p $WORKDIR
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 # 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 8 --output trinity-fish2 --full_cleanup</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 /tmp <code>$ cd /tmp
-$ wget "https://github.com/trinityrnaseq/trinityrnaseq/archive/v2.0.6.tar.gz" -O trinity-v2.0.6.tar.gz +$ wget https://github.com/trinityrnaseq/trinityrnaseq/releases/download/Trinity-v2.6.6/Trinityrnaseq-v2.6.6.wExtSampleData.tar.gz 
-$ tar -xvf trinity-v2.0.6.tar.gz +$ tar xf Trinityrnaseq-v2.6.6.wExtSampleData.tar.gz 
-$ cd trinityrnaseq-2.0.6+$ cd Trinityrnaseq-v2.6.6 
-$ scl enable devtoolset-2 bash +$ make 
-CC=clang make +$ make plugins 
-CC=clang make plugins +$ sudo yum install numpy 
-$ sudo mkdir /export/apps/trinity/v2.0.6 +$ sudo mkdir /export/apps/trinity/v2.6.6 
-$ cp -r /export/apps/trinity/v2.0.6 +make test_trinity 
-$ sudo chown -R root:root /export/apps/trinity/v2.0.6</code>+$ sudo cp -r /export/apps/trinity/v2.6.6</code> 
 + 
 +Consult the [[https://github.com/trinityrnaseq/trinityrnaseq/wiki/Installing-Trinity|installing Trinity]] guide in the documentation, although it misses some dependencies!
trinity-software.txt · Last modified: 2020/10/28 11:28 by aorth