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rsem-software [2015/02/11 14:34]
joguya created
rsem-software [2015/07/23 17:00] (current)
joguya
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(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