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#42 How exactly should I install the newest version of MOCAT2 from the github?

Done
nobody
Github (1)
Medium
Defect
2017-07-31
2017-01-23
Silas Kieser
No

Hello

How exactly should I install the newest version of MOCAT2 from the github?

I downloaded the repro as zip and found the instalation files in dev/public/setup
when I run setup.MOCAT2.pl I got an error that the script is not in the main folder, so I placed it in dev/public
I could install but when I run the program I got an error:

Can't locate MOCATUnpublished.pm in @INC (@INC contains: /nihs/Bioinformatics/nrc_hmi/Public/Programs/mocat2/dev/public/src /nihs/Bioinformatics/nrc_hmi/Public/Programs/mocat2/dev/public/src /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at /nihs/Bioinformatics/nrc_hmi/Public/Programs/mocat2/dev/public/src/MOCAT.pl line 31.

Kind regard
Silas

Discussion

  • MOCAT

    MOCAT - 2017-01-23

    MOCAT2 dev is not tested for being installed and does require a little more manual labor to get to work. As I have time I may change this in the future.

    You have to add the path to the Unpublished.pm file into your perl 5 path as:
    export PERL5LIB=<PATH to="" Unpublished.pm="">:$PERL5LIB

     

  • MOCAT

    MOCAT - 2017-01-27
    • status: New --> Done
     

  • Silas Kieser

    Silas Kieser - 2017-07-31

    Can you explain me again, what should I do to use the developpment version?
    Should I use dev/public
    or dev/unpublished

    Which setup scripts do I have to use?

    Kidn regards
    Silas

     

    • MOCAT

      MOCAT - 2017-07-31

      Just copy the folders into the same folders as you installed MOCAT. No need
      to re-run any other scripts. Please note that I cannot provide any support
      beyond this right now as I'm not actively developing MOCAT anymore. Good
      luck!

      Jens Roat Kultima, Ph.D.

      Computational Scientist
      Janssen Human Microbiome Institute
      Janssen Pharmaceuticals
      255 Main Street, 10th Floor
      Cambridge, MA 02142

      On Mon, Jul 31, 2017 at 10:13 AM, Silas Kieser silask@users.sf.net wrote:

      Can you explain me again, what should I do to use the developpment version?
      Should I use dev/public
      or dev/unpublished

      Which setup scripts do I have to use?

      Kidn regards
      Silas

      [tickets:#42] How exactly should I install the newest version of
      MOCAT2 from the github?

      Status: Done
      Labels: Github
      Created: Mon Jan 23, 2017 11:16 AM UTC by Silas Kieser
      Last Updated: Fri Jan 27, 2017 05:18 PM UTC
      Owner: nobody

      Hello

      How exactly should I install the newest version of MOCAT2 from the github?

      I downloaded the repro as zip and found the instalation files in
      dev/public/setup
      when I run setup.MOCAT2.pl I got an error that the script is not in the
      main folder, so I placed it in dev/public
      I could install but when I run the program I got an error:

      ~~~
      Can't locate MOCATUnpublished.pm in @INC (@INC contains:
      /nihs/Bioinformatics/nrc_hmi/Public/Programs/mocat2/dev/public/src
      /nihs/Bioinformatics/nrc_hmi/Public/Programs/mocat2/dev/public/src
      /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl
      /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at
      /nihs/Bioinformatics/nrc_hmi/Public/Programs/mocat2/dev/public/src/MOCAT.pl
      line 31.
      ~~~

      Kind regard
      Silas

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