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rsem-software
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rsem-software [2015/02/11 14:34] joguya created |
rsem-software [2015/07/23 17:00] (current) joguya |
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| ====== RSEM ====== | ====== RSEM ====== | ||
| - | * RSEM(RNA-Seq by Expectation-Maximization) is an accurate quantification of gene and isoform expression from RNA-Seq data. | + | RSEM(RNA-Seq by Expectation-Maximization) is an accurate quantification of gene and isoform expression from RNA-Seq data. |
| - | ==== v1.2.9 ==== | + | * Version: 1.2.21 |
| - | * Version: 1.2.9 | + | |
| * Added: February, 2015 | * Added: February, 2015 | ||
| + | * Updated: July, 2015 | ||
| * Link: http://deweylab.biostat.wisc.edu/rsem/ | * Link: http://deweylab.biostat.wisc.edu/rsem/ | ||
| === Usage === | === Usage === | ||
| * Show all available versions of RSEM<code>module avail RSEM</code> | * Show all available versions of RSEM<code>module avail RSEM</code> | ||
| - | * Load RSEM module: <code>module load RSEM/1.24</code> | + | * Load RSEM module: <code>module load RSEM/1.2.21</code> |
| === Installation === | === Installation === | ||
| - | * clone RSEM repo & compile it<code>git clone https://github.com/bli25wisc/RSEM.git | + | *Download & build/compile it<code> |
| - | cd RSEM | + | wget http://deweylab.biostat.wisc.edu/rsem/src/rsem-1.2.21.tar.gz |
| - | git checkout v1.2.9 | + | tar -xvf rsem-1.2.21.tar.gz |
| - | module load bowtie2/2.2.3 bowtie/1.1.1 | + | cd rsem-1.2.21 |
| + | scl enable devtoolset-2 bash | ||
| + | module load bowtie2 | ||
| make | make | ||
| - | sudo mkdir -p /export/apps/RSEM/1.2.9/ | + | sudo mkdir /export/apps/RSEM/1.2.21/ |
| - | sudo cp -r . /export/apps/RSEM/1.2.9/ | + | sudo cp -r . /export/apps/RSEM/1.2.21/ |
| </code> | </code> | ||
| - | * RSEM module file<code> | ||
| - | #%Module1.0 | ||
| - | ##################################################################### | ||
| - | ## | ||
| - | ## RSEM Modulefile | ||
| - | ## By James Oguya, j.oguya@cgiar.org | ||
| - | ## February, 2015 | ||
| - | ## | ||
| - | |||
| - | set appname RSEM | ||
| - | set version 1.2.9 | ||
| - | set prefix /export/apps/${appname}/${version} | ||
| - | set exec_prefix ${prefix} | ||
| - | set url "http://deweylab.biostat.wisc.edu/rsem/" | ||
| - | set msg "RSEM(RNA-Seq by Expectation-Maximization): accurate quantification of gene and isoform expression from RNA-Seq data.\nRSEM Official Site: $url\n" | ||
| - | |||
| - | module-whatis "$msg" | ||
| - | |||
| - | proc ModulesHelp { } { | ||
| - | puts stderr "$msg" | ||
| - | } | ||
| - | |||
| - | conflict RSEM | ||
| - | |||
| - | prepend-path PATH ${exec_prefix} | ||
| - | |||
| - | # load RSEM dependencies - bowtie2/2.2.3, bowtie/1.1.1, R/3.1.0 | ||
| - | if { ! [is-loaded bowtie2/2.2.3] } { | ||
| - | module load bowtie2/2.2.3 | ||
| - | } | ||
| - | |||
| - | if { ![is-loaded bowtie/1.1.1] } { | ||
| - | module load bowtie/1.1.1 | ||
| - | } | ||
| - | |||
| - | if { ![is-loaded R/3.1.0] } { | ||
| - | module load R/3.1.0 | ||
| - | }</code> | ||
| - | |||
| - | * deploy the new module using ansible<code>ansible-playbook site.yml -u provisioning -K -s --limit=compute --tags=modules</code> | ||
| - | |||
rsem-software.txt · Last modified: 2015/07/23 17:00 by joguya
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