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trinity-software [2015/07/31 11:59] – joguyatrinity-software [2016/01/28 10:31] – joguya
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 ===== Information ===== ===== Information =====
  
-  * Version: v2.0.6+  * Latest Version: v2.1.1 
 +  * Updated: January, 2016
   * Added: March, 2015   * Added: March, 2015
   * Link: https://trinityrnaseq.github.io   * Link: https://trinityrnaseq.github.io
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 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:** **Note:**
-  * 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. +  * 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: +  * 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
- +
-<code>#!/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/v2.1.1
 module load bowtie/1.1.1 module load bowtie/1.1.1
 module load samtools/1.2 module load samtools/1.2
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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</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/archive/v2.1.1.tar.gz" -O trinity-v2.1.1.tar.gz 
-$ tar -xvf trinity-v2.0.6.tar.gz +$ tar -xvf v2.1.1.tar.gz 
-$ cd trinityrnaseq-2.0.6/+$ cd trinityrnaseq-2.1.1
 $ scl enable devtoolset-2 bash $ scl enable devtoolset-2 bash
 $ CC=clang make $ CC=clang make
 $ CC=clang make plugins $ CC=clang make plugins
-$ sudo mkdir /export/apps/trinity/v2.0.6 +$ sudo mkdir /export/apps/trinity/v2.1.1 
-$ cp -r * /export/apps/trinity/v2.0.6 +$ sudo cp -r . /export/apps/trinity/v2.1.1/ 
-$ sudo chown -R root:root /export/apps/trinity/v2.0.6</code>+</code>
trinity-software.txt · Last modified: 2020/10/28 11:28 by aorth