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rsem-software [2015/02/11 11:34]
joguya created
rsem-software [2018/11/18 08:02] (current)
aorth
Line 1: Line 1:
 ====== RSEM ====== ====== RSEM ======
-  * RSEM(RNA-Seq by Expectation-Maximization) is an accurate quantification of gene and isoform expression from RNA-Seq data.+RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data.
  
-==== v1.2.9 ==== +  * Version: 1.3.1
-  * Version: 1.2.9+
   * Added: February, 2015   * Added: February, 2015
-  * Link: http://deweylab.biostat.wisc.edu/rsem/+  * Updated: November, 2018 
 +  * Link: https://deweylab.github.io/RSEM/
  
 === Usage === === Usage ===
-  * Show all available versions of RSEM<code>module avail RSEM</code> +Show all available versions:
-  * Load RSEM module<code>module load RSEM/1.24</code>+
  
-=== Installation === +<code>module avail RSEM</code>
-  * clone RSEM repo & compile it<code>git clone https://github.com/bli25wisc/RSEM.git +
-cd RSEM +
-git checkout v1.2.9 +
-module load bowtie2/2.2.3 bowtie/1.1.1 +
-make +
-sudo mkdir -p /export/apps/RSEM/1.2.9/ +
-sudo cp -r . /export/apps/RSEM/1.2.9/ +
-</code> +
-  * RSEM module file<code> +
-#%Module1.0 +
-##################################################################### +
-## +
-## RSEM Modulefile +
-## By James Oguya, j.oguya@cgiar.org +
-## February, 2015 +
-##+
  
-set appname         RSEM +Load one version into your environment: 
-set version         1.2.9 +<code>module load RSEM/1.3.1</code>
-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 "$msg" +=== Installation === 
- +Notes from the sysadmin during installation:
-proc ModulesHelp { } { +
-    puts stderr "$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>+
  
 +<code>$ cd /tmp
 +$ wget https://github.com/deweylab/RSEM/archive/v1.3.1.tar.gz
 +$ tar xf v1.3.1.tar.gz
 +$ cd RSEM-1.3.1
 +$ sudo yum install gcc-c++
 +$ make
 +$ sudo mkdir -p /export/apps/RSEM/1.3.1
 +$ sudo chown aorth /export/apps/RSEM/1.3.1
 +$ make prefix=/export/apps/RSEM/1.3.1 install
 +$ sudo chown -R root:root /export/apps/RSEM/1.3.1</code>
rsem-software.1423654471.txt.gz · Last modified: 2015/02/11 11:34 by joguya