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--- rsem-software [2015/07/23 14:00] – 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.
-  * Version: 1.2.21
+  * Version: 1.3.3
   * Added: February, 2015
-  * Updated: July, 2015
+  * Updated: July, 2025
-  * Link: http://deweylab.biostat.wisc.edu/rsem/
+  * 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/1.2.21</code>
+<code>$ module avail RSEM</code>
+Load one version into your environment:
+<code>$ module load RSEM/1.3.3</code>
 === Installation ===
-  *Download & build/compile it<code>
+Notes from the sysadmin during installation:
-wget http://deweylab.biostat.wisc.edu/rsem/src/rsem-1.2.21.tar.gz
-tar -xvf rsem-1.2.21.tar.gz
+<code>$ cd /var/scratch
-cd rsem-1.2.21
+$ wget https://github.com/deweylab/RSEM/archive/v1.3.3.tar.gz
-scl enable devtoolset-2 bash
+$ tar xf v1.3.3.tar.gz
-module load bowtie2
+$ cd RSEM-1.3.3
-make
+$ make
-sudo mkdir /export/apps/RSEM/1.2.21/
+$ sudo mkdir -p /export/apps/RSEM/1.3.3
-sudo cp -r . /export/apps/RSEM/1.2.21/
+$ sudo chown aorth /export/apps/RSEM/1.3.3
-</code>
+$ make prefix=/export/apps/RSEM/1.3.3 install
+$ sudo chown -R root:root /export/apps/RSEM/1.3.3</code>