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trinity-software [2015/03/24 17:02] – aorthtrinity-software [2020/10/28 11:28] (current) – aorth
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 ===== Information ===== ===== Information =====
  
-  * Version: v2.0.6+  * Latest Version: v2.11.0
   * Added: March, 2015   * Added: March, 2015
 +  * Updated: October, 2020
   * Link: https://trinityrnaseq.github.io   * Link: https://trinityrnaseq.github.io
  
 ===== Usage ===== ===== 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>
  
-**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: +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 
-<code>#!/bin/env bash+  * 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 -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 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 8 --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> +<code>$ cd /tmp 
-$ sudo su - provisioning +$ wget https://github.com/trinityrnaseq/trinityrnaseq/releases/download/v2.11.0/trinityrnaseq-v2.11.0.FULL.tar.gz 
-$ cd src +$ tar xf trinityrnaseq-v2.11.0.FULL.tar.gz 
-$ wget "https://github.com/trinityrnaseq/trinityrnaseq/archive/v2.0.6.tar.gz" -O trinity-v2.0.6.tar.gz +$ cd trinityrnaseq-v2.11.0 
-$ tar -xvf trinity-v2.0.6.tar.gz +$ sed -i 's/cmake/cmake3/' Chrysalis/Makefile Inchworm/Makefile 
-$ cd trinityrnaseq-2.0.6/ +$ make 
-$ scl enable devtoolset-2 bash +$ make plugins 
-$ CC=clang make +$ sudo yum install python36-numpy.x86_64 
-$ CC=clang make plugins +$ sudo mkdir -p /export/apps/trinity/v2.11.0 
-$ sudo mkdir /export/apps/trinity/v2.0.6 +$ sudo cp -r . /export/apps/trinity/v2.11.0 
-$ sudo chown -R provisioning:provisioning /export/apps/trinity/v2.0.6 +$ export TRINITY_HOME=/export/apps/trinity/v2.11.0 
-$ cp -r * /export/apps/trinity/v2.0.6 +$ module load samtools/1.9 salmon/1.3.0 bowtie2/2.3.4.1 jellyfish/2.3.0 
-$ sudo chown -R root:root /export/apps/trinity/v2.0.6 +$ cd sample_data/test_Trinity_Assembly 
-</code>+$ ./runMe.sh</code> 
 + 
 +Consult the [[https://github.com/trinityrnaseq/trinityrnaseq/wiki/Installing-Trinity|installing Trinity]] guide in the documentation.
trinity-software.1427216538.txt.gz · Last modified: 2015/03/24 17:02 by aorth