This page was last updated on Friday, 23-Dec-2016 10:51:16 CST

Installation notes for RSEM version 1.3.0

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Prerequisites

C++, Perl and R are required to be installed.

To use the --gff3 option of rsem-prepare-reference, Python is also required to be installed.

To take advantage of RSEM's built-in support for the Bowtie/Bowtie 2/STAR alignment program, you must have Bowtie/Bowtie 2/STAR installed.

Installation

1. $ ver="1.3.0"
2. $ cd /programinstallers/
3. $ wget -N https://github.com/deweylab/RSEM/archive/v$ver.tar.gz
4. $ mv v$ver.tar.gz rsem-v$ver.tar.gz
5. $ cd /usr/local/bin
6. $ tar -zxvf /programinstallers/rsem-v$ver.tar.gz
7. $ cd RSEM-$ver
8. $ make
9. EBSeq and blockmodeling install, note that this will not update an existing version
   $ make ebseq
10. $ cd ..
11. Make a version-independent symlink
    $ ln -s RSEM-$ver rsem
12. Add to default PATH
    $ sudo nano /etc/profile
    …
    PATH="$PATH:/usr/local/bin/rsem"
    …
13. Cleanup. Remove most of the source code
    $ rm rsem/*.{cpp,h,o}
14. $ rm rsem/boost -rf
15. $ rm rsem/sam/*.{c,h,o} sam/bcftools/*.{c,h,o}