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rsem-software [2015/02/11 14:34]
joguya created
rsem-software [2018/11/18 11:00]
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 and run it: 
-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.txt · Last modified: 2018/11/18 11:02 by aorth