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trinity-software [2017/08/22 12:20]
aorth
trinity-software [2020/10/28 11:28] (current)
aorth
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 ===== Information ===== ===== Information =====
  
-  * Latest Version: v2.4.0+  * Latest Version: v2.11.0
   * Added: March, 2015   * Added: March, 2015
-  * Updated: August2017+  * Updated: October2020
   * 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>
  
-**Note:** +Load one version into your environment and run it: 
-  * 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. +<code>$ module load trinity/v2.11.0 
-  * 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+$ Trinity</code> 
 + 
 +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 
 +  * 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/v2.4.0+module load trinity/v2.6.6
  
 # create and change to a working directory on the compute node # create and change to a working directory on the compute node
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 <code>$ cd /tmp <code>$ cd /tmp
-$ wget https://github.com/trinityrnaseq/trinityrnaseq/archive/Trinity-v2.4.0.zip +$ wget https://github.com/trinityrnaseq/trinityrnaseq/releases/download/v2.11.0/trinityrnaseq-v2.11.0.FULL.tar.gz 
-unzip Trinity-v2.4.0.zip +tar xf trinityrnaseq-v2.11.0.FULL.tar.gz 
-$ cd trinityrnaseq-Trinity-v2.4.0 +$ cd trinityrnaseq-v2.11.0 
-scl enable devtoolset-4 bash+sed -i 's/cmake/cmake3/' Chrysalis/Makefile Inchworm/Makefile
 $ make $ make
 $ make plugins $ make plugins
-$ sudo mkdir /export/apps/trinity/v2.4.0 +$ sudo yum install python36-numpy.x86_64 
-$ make test_trinity +$ sudo mkdir -p /export/apps/trinity/v2.11.0 
-$ sudo cp -r . /export/apps/trinity/v2.4.0</code>+$ 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.1503404455.txt.gz · Last modified: 2017/08/22 12:20 by aorth