Table of Contents
Trinity 2.4.0¶
- Installation date: 01/03/2017
- URL: https://github.com/trinityrnaseq/trinityrnaseq/wiki
- Apolo version: Apolo II
- License: Copyright (c) 2014, trinityrnaseq
Dependencies¶
- GNU Gcc >= 4.9.4
- Intel Parallel Studio XE Cluster Edition 2017 Update 1
- bowtie2 >= 2.3.0
- ncbi-blast+ >= 2.6.0
- R and edgeRsource(”https://bioconductor.org/biocLite.R”)
- r >= 3.3.
- edgeR
- DESeq2
- ROTS
- qvalue
- goseq
Installation¶
After solving the aforementioned dependencies, you can proceed with the installation of Trinity.
- Download the binaries
wget https://github.com/trinityrnaseq/trinityrnaseq/archive/Trinity-v2.4.0.tar.gz
tar xf Trinity-v2.4.0.tar.gz
- Compilation (makefile)
cd trinityrnaseq-Trinity-v2.4.0/
module load intel/2017_update-1
#change -openmp for -fopenmp in the following scripts
emacs Chrysalis/Makefile_icpc
emacs Inchworm/configure
emacs trinity-plugins/parafly-code/configure
emacs trinity-plugins/parafly-code/configure.ac
make TRINITY_COMPILER=intel 2>&1 | tee trinity-make.log
make TRINITY_COMPILER=intel plugins 2>&1 | tee trinity-make-plugins.log
- Test the installation
module load ncbi-blast/2.6.0_x86_64
module load bowtie2/2.3.0_intel-2017_update-1
cd sample_data/test_Trinity_Assembly/
./runMe.sh
Module¶
#%Module1.0#####################################################################
##
## module trinity/2.4.0_intel-2017_update-1
##
## /share/apps/modules/trinity/2.4.0_intel-2017_update-1 Written by Mateo Gomez-Zuluaga
##
proc ModulesHelp { } {
puts stderr "\ttrinity/2.4.0_intel-2017_update-1 - sets the Environment for Trinity in \
\n\tthe share directory /share/apps/trinity/2.4.0/intel/2017_update-1\n"
}
module-whatis "\n\n\tSets the environment for using Trinity 2.4.0 \
\n\tbuilded with Intel Parallel Studio XE 2017\n"
# for Tcl script use only
set topdir /share/apps/trinity/2.4.0/intel/2017_update-1
set version 2.4.0
set sys x86_64-redhat-linux
conflict trinity
module load gcc/4.9.4
module load bowtie2/2.3.0_intel-2017_update-1
module load ncbi-blast/2.6.0_x86_64
module load r/3.3.2_intel_mkl_2017_update-1
prepend-path PATH $topdir
Usage mode¶
module load trinity/2.4.0_intel-2017_update-1