by
Thu, Mar 21 2013 06:31:34

GATK v2.0 not open source

The new GATK v2.0 software was released under a non-open source licence, and initially had some rather onerous restrictions (July/Aug 2012). GATK Lite was introduced as an MIT open source continuation of GATK v1, in Jan 2013, the Broad announced plans to drop the open source GATK Lite.

  1. pmelsted
    Pall Melsted@pmelsted
    GATK licensing snafu is a shame, I was just beginning to like it. Won't invest any time extending/developing unless there is an OS fork
    Thu, Mar 21 2013 02:38:59
  2. gatk_dev
    GATK Dev Team@gatk_dev
    @stuka No, we've been putting in a lot of effort to cover the codebase with unit tests to vastly improve reliability. ETA Monday 2/25.
    Fri, Feb 22 2013 13:21:52
  3. stuka
    Stuart Glenn@stuka
    Wasn't GATK 2.4 supposed to be out awhile ago? Did they decide to dick up the license some more?
    Fri, Feb 22 2013 08:55:17
  4. sjackman
    Shaun Jackman@sjackman
    RT @pjacock: Sanger job on #samtools to “reestablish it as a pre-eminent tool for the genomics community” https://jobs.sanger.ac.uk/wd/plsql/wd_portal.show_job?p_web_site_id=1764&p_web_page_id=161360 (Sanger’s GATK plan B?)
    Mon, Feb 18 2013 08:44:54
  5. kevinltweets
    Kevin Lam@kevinltweets
    why licensing of GATK to commercial entities is bad: wp.me/p1PnkE-2g via @wordpressdotcom
    Mon, Feb 18 2013 07:53:19
  6. BioMickWatson
    Mick Watson@BioMickWatson
    The Appistry team set the record straight - comment on my blog: biomickwatson.wordpress.com/2013/01/28/gat… #GATK
    Mon, Feb 18 2013 04:10:41
  7. gedankenstuecke
    Bastian Greshake@gedankenstuecke
    RT @pjacock: Sanger job on #samtools to “reestablish it as a pre-eminent tool for the genomics community” https://jobs.sanger.ac.uk/wd/plsql/wd_portal.show_job?p_web_site_id=1764&p_web_page_id=161360 (Sanger’s GATK plan B?)
    Fri, Feb 15 2013 09:25:58
  8. Massgenomics
    Massgenomics@Massgenomics
    RT @pjacock: Sanger job on #samtools to “reestablish it as a pre-eminent tool for the genomics community” https://jobs.sanger.ac.uk/wd/plsql/wd_portal.show_job?p_web_site_id=1764&p_web_page_id=161360 (Sanger’s GATK plan B?)
    Fri, Feb 15 2013 09:22:33
  9. gatk_dev
    GATK Dev Team@gatk_dev
    @jmchilton @BioMickWatson Don't know about requires, but very helpful? Maybe with support you could switch to #GATK 2? v1 is obsolete now...
    Fri, Feb 15 2013 08:13:16
  10. evolvability
    David Mittelman@evolvability
    RT @pjacock: Sanger job on #samtools to “reestablish it as a pre-eminent tool for the genomics community” https://jobs.sanger.ac.uk/wd/plsql/wd_portal.show_job?p_web_site_id=1764&p_web_page_id=161360 (Sanger’s GATK plan B?)
    Fri, Feb 15 2013 08:08:06
  11. jmchilton
    John Chilton@jmchilton
    Commenter @ @BioMickWatson's blog claims CLIA #genomics requires commercial tools&support. #false We are doing it with GATK 1 and #usegalaxy
    Fri, Feb 15 2013 06:28:29
  12. pjacock
    Peter Cock@pjacock
    RT @BioMickWatson: Comments on my blog suggest $40k per annum for GATK - can anyone compare? biomickwatson.wordpress.com/2013/01/28/gat…
    Fri, Feb 15 2013 05:09:23
  13. sebhtml
    Sébastien Boisvert@sebhtml
    RT @pjacock: Sanger job on #samtools to “reestablish it as a pre-eminent tool for the genomics community” https://jobs.sanger.ac.uk/wd/plsql/wd_portal.show_job?p_web_site_id=1764&p_web_page_id=161360 (Sanger’s GATK plan B?)
    Fri, Feb 15 2013 04:43:06
  14. BioMickWatson
    Mick Watson@BioMickWatson
    Comments on my blog suggest $40k per annum for GATK - can anyone compare? biomickwatson.wordpress.com/2013/01/28/gat…
    Fri, Feb 15 2013 04:34:16
  15. agapow
    Paul-Michael Agapow@agapow
    RT @pjacock: Sanger job on #samtools to “reestablish it as a pre-eminent tool for the genomics community” https://jobs.sanger.ac.uk/wd/plsql/wd_portal.show_job?p_web_site_id=1764&p_web_page_id=161360 (Sanger’s GATK plan B?)
    Fri, Feb 15 2013 04:17:15
  16. yokofakun
    Pierre Lindenbaum@yokofakun
    RT @pjacock: Sanger job on #samtools to “reestablish it as a pre-eminent tool for the genomics community” https://jobs.sanger.ac.uk/wd/plsql/wd_portal.show_job?p_web_site_id=1764&p_web_page_id=161360 (Sanger’s GATK plan B?)
    Fri, Feb 15 2013 04:14:08
  17. pjacock
    Peter Cock@pjacock
    Sanger job on #samtools to “reestablish it as a pre-eminent tool for the genomics community” https://jobs.sanger.ac.uk/wd/plsql/wd_portal.show_job?p_web_site_id=1764&p_web_page_id=161360 (Sanger’s GATK plan B?)
    Fri, Feb 15 2013 04:12:32
  18. BioMickWatson
    Mick Watson@BioMickWatson
    @MatthewBStocks @drchriscole @gatk_dev @notSoJunkDNA or perhaps the user list is sent to Appistry ;) #justkidding
    Fri, Feb 15 2013 03:59:36
  19. pjacock
    Peter Cock@pjacock
    Needn’t be from scratch if fork existing MIT licensed codebase RT @dgmacarthur: @BioMickWatson Have fun rebuilding GATK from scratch, dude.
    Wed, Feb 13 2013 01:51:04
  20. BioMickWatson
    Mick Watson@BioMickWatson
    @gatk_dev @dgmacarthur @evolvability we discussed this yesterday - plenty of papers on software claiming to outperform GATK
    Tue, Feb 12 2013 23:38:47
  21. BioMickWatson
    Mick Watson@BioMickWatson
    @gatk_dev @dgmacarthur @evolvability I guess what the commenter is trying to say is that there are alternatives :-)
    Tue, Feb 12 2013 23:37:48
  22. sebhtml
    Sébastien Boisvert@sebhtml
    RT @evolvability: @gatk_dev @dgmacarthur @BioMickWatson agree, although in my case, i prefer to spend my research dollars developing something new...
    Tue, Feb 12 2013 19:46:40
  23. evolvability
    David Mittelman@evolvability
    @evolvability @gatk_dev @dgmacarthur @BioMickWatson new as in something other than a reproduction of an existing tool that works well...
    Tue, Feb 12 2013 19:20:39
  24. evolvability
    David Mittelman@evolvability
    @gatk_dev @dgmacarthur @BioMickWatson agree, although in my case, i prefer to spend my research dollars developing something new...
    Tue, Feb 12 2013 19:12:22
  25. evolvability
    David Mittelman@evolvability
    RT @gatk_dev: @dgmacarthur @evolvability @BioMickWatson Could write new walkers to work on top of GATK framework (MIT-free). Save *some* effort.
    Tue, Feb 12 2013 19:10:40

Did you find this story interesting? Be the first to or comment.

Liked!

Peter Cock

Bioinformatian working in the UK, doing genome analysis etc, one of the major developers on @Biopython.

4stories
5followers
1following
Total views
459

Sorry.

This URL is already in use. Please choose another URL.
Edit URL

Storify

@Storify

Are you sure?

Are you sure you want to delete this story?

Are you sure?

Are you sure you want to flag this story?