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--- rsem-software [2015/02/11 11:34] – created joguya
+++ rsem-software [2025/07/22 18:50] (current) – aorth
@@ Line 1: / Line 1: @@
 ====== 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: 1.3.3
-  * Version: 1.2.9
   * Added: February, 2015
-  * Link: http://deweylab.biostat.wisc.edu/rsem/
+  * Updated: July, 2025
+  * Link: https://deweylab.github.io/RSEM/
 === 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/1.3.3</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 /var/scratch
+$ wget https://github.com/deweylab/RSEM/archive/v1.3.3.tar.gz
+$ tar xf v1.3.3.tar.gz
+$ cd RSEM-1.3.3
+$ make
+$ sudo mkdir -p /export/apps/RSEM/1.3.3
+$ sudo chown aorth /export/apps/RSEM/1.3.3
+$ make prefix=/export/apps/RSEM/1.3.3 install
+$ sudo chown -R root:root /export/apps/RSEM/1.3.3</code>