This page was last updated on Thursday, 21-Jul-2022 10:16:00 CDT

Installation notes for subread version 1.3.1

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Prerequisites

None

Installation

1. $ ver="2.0.3"
2. $ cd /programinstallers/
3. $ wget -N https://sourceforge.net/projects/subread/files/subread-${ver}/subread-${ver}-source.tar.gz
4. $ tar -zxvf subread-${ver}-source.tar.gz
5. $ cd subread-$ver-source/src
6. $ make -f Makefile.Linux
7. $ cd ../bin
8. $ mkdir /usr/local/bin/subread
9. $ cp -puvr * /usr/local/bin/subread/

   'exactSNP' -> '/usr/local/bin/subread/exactSNP'
   'featureCounts' -> '/usr/local/bin/subread/featureCounts'
   'subindel' -> '/usr/local/bin/subread/subindel'
   'subjunc' -> '/usr/local/bin/subread/subjunc'
   'sublong' -> '/usr/local/bin/subread/sublong'
   'subread-align' -> '/usr/local/bin/subread/subread-align'
   'subread-buildindex' -> '/usr/local/bin/subread/subread-buildindex'
   'utilities' -> '/usr/local/bin/subread/utilities'
   'utilities/genRandomReads' -> '/usr/local/bin/subread/utilities/genRandomReads'
   'utilities/detectionCall' -> '/usr/local/bin/subread/utilities/detectionCall'
   'utilities/repair' -> '/usr/local/bin/subread/utilities/repair'
   'utilities/txUnique' -> '/usr/local/bin/subread/utilities/txUnique'
   'utilities/removeDup' -> '/usr/local/bin/subread/utilities/removeDup'
   'utilities/qualityScores' -> '/usr/local/bin/subread/utilities/qualityScores'
   'utilities/subread-fullscan' -> '/usr/local/bin/subread/utilities/subread-fullscan'
   'utilities/propmapped' -> '/usr/local/bin/subread/utilities/propmapped'
   'utilities/flattenGTF' -> '/usr/local/bin/subread/utilities/flattenGTF'

10. $ cd ../../
11. $ cp -puv doc/SubreadUserGuide.pdf /programinstallers/web/subread/
12. $ rm subread-$ver-source -rf
13. Add to default PATH
    $ sudo nano /etc/profile
    ...
    PATH="$PATH:/usr/local/bin/subread"
    ...