rsem-software
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rsem-software [2015/02/11 11:34] – created joguya | rsem-software [2018/11/18 08:02] (current) – aorth | ||
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====== RSEM ====== | ====== RSEM ====== | ||
- | * RSEM(RNA-Seq by Expectation-Maximization) | + | RSEM is a software package for estimating |
- | ==== v1.2.9 ==== | + | |
- | | + | |
* Added: February, 2015 | * Added: February, 2015 | ||
- | * Link: http:// | + | |
+ | | ||
=== Usage === | === Usage === | ||
- | * Show all available versions | + | Show all available versions: |
- | * Load RSEM module: < | + | |
- | === Installation === | + | < |
- | * clone RSEM repo & compile it< | + | |
- | cd RSEM | + | |
- | git checkout v1.2.9 | + | |
- | module | + | |
- | make | + | |
- | sudo mkdir -p / | + | |
- | sudo cp -r . / | + | |
- | </ | + | |
- | * RSEM module file< | + | |
- | # | + | |
- | ##################################################################### | + | |
- | ## | + | |
- | ## RSEM Modulefile | + | |
- | ## By James Oguya, j.oguya@cgiar.org | + | |
- | ## February, 2015 | + | |
- | ## | + | |
- | set appname | + | Load one version |
- | set version | + | < |
- | set prefix | + | |
- | set exec_prefix | + | |
- | set url " | + | |
- | set msg " | + | |
- | module-whatis " | + | === Installation === |
- | + | Notes from the sysadmin during installation: | |
- | proc ModulesHelp { } { | + | |
- | puts stderr " | + | |
- | } | + | |
- | + | ||
- | conflict | + | |
- | + | ||
- | prepend-path | + | |
- | + | ||
- | # load RSEM dependencies - bowtie2/ | + | |
- | if { ! [is-loaded bowtie2/ | + | |
- | module load bowtie2/ | + | |
- | } | + | |
- | + | ||
- | if { ![is-loaded bowtie/ | + | |
- | module load bowtie/ | + | |
- | } | + | |
- | + | ||
- | if { ![is-loaded R/3.1.0] } { | + | |
- | module load R/3.1.0 | + | |
- | }</ | + | |
- | + | ||
- | * deploy | + | |
+ | < | ||
+ | $ wget https:// | ||
+ | $ tar xf v1.3.1.tar.gz | ||
+ | $ cd RSEM-1.3.1 | ||
+ | $ sudo yum install gcc-c++ | ||
+ | $ make | ||
+ | $ sudo mkdir -p / | ||
+ | $ sudo chown aorth / | ||
+ | $ make prefix=/ | ||
+ | $ sudo chown -R root:root / |
rsem-software.1423654471.txt.gz · Last modified: 2015/02/11 11:34 by joguya