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trinity-software [2015/03/20 15:32]
aorth [Usage]
trinity-software [2020/10/28 11:28] (current)
aorth
Line 4: Line 4:
 ===== Information ===== ===== Information =====
  
-  * Version: v2.0.3 +  * Latest Version: v2.11.0 
-  * Added: February2014+  * Added: March, 2015 
 +  * Updated: October2020
   * 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 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 10+#SBATCH -n 8
  
-module load trinity/v2.0.+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=$SLURM_JOBID+export WORKDIR=/var/scratch/$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 --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/releases/download/v2.11.0/trinityrnaseq-v2.11.0.FULL.tar.gz 
-$ tar xf v2.0.3.tar.gz +$ tar xf trinityrnaseq-v2.11.0.FULL.tar.gz 
-$ cd trinityrnaseq-2.0.3 +$ cd trinityrnaseq-v2.11.0 
-$ sudo mkdir /export/apps/trinity/v2.0.3 +sed -i 's/cmake/cmake3/' Chrysalis/Makefile Inchworm/Makefile
-$ 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 yum install python36-numpy.x86_64 
 +$ sudo mkdir -p /export/apps/trinity/v2.11.0 
 +$ sudo cp -r . /export/apps/trinity/v2.11.0 
 +$ export TRINITY_HOME=/export/apps/trinity/v2.11.0 
 +$ module load samtools/1.9 salmon/1.3.0 bowtie2/2.3.4.1 jellyfish/2.3.0 
 +$ cd sample_data/test_Trinity_Assembly 
 +$ ./runMe.sh</code> 
 + 
 +Consult the [[https://github.com/trinityrnaseq/trinityrnaseq/wiki/Installing-Trinity|installing Trinity]] guide in the documentation.
trinity-software.1426865550.txt.gz · Last modified: 2015/03/20 15:32 by aorth