https://github.com/sanger-pathogens/gubbins
Tip revision: c5c8decee2fda6a3696d12b0e2c8bb922a2b95f8 authored by andrewjpage on 13 January 2016, 11:31:14 UTC
Merge pull request #160 from andrewjpage/remove_install_sh
Merge pull request #160 from andrewjpage/remove_install_sh
Tip revision: c5c8dec
CHANGELOG
gubbins (1.3.4~trusty1) trusty; urgency=low
* Identify blocks at end of genome
-- Andrew Page <ap13@sanger.ac.uk> Mon, 18 Apr 2015 14:51:00 +0000
gubbins (1.3.3~trusty1) trusty; urgency=low
* Max window size arg bug
-- Andrew Page <ap13@sanger.ac.uk> Thu, 16 Apr 2015 16:09:00 +0000
gubbins (1.3.2~trusty1) trusty; urgency=low
* pass in self to window size check
-- Andrew Page <ap13@sanger.ac.uk> Thu, 16 Apr 2015 16:00:00 +0000
gubbins (1.3.1~trusty1) trusty; urgency=low
* Calculate bases used for clonal frame
-- Andrew Page <ap13@sanger.ac.uk> Thu, 16 Apr 2015 15:00:00 +0000
gubbins (1.3.0~trusty1) trusty; urgency=low
* Apply filtering to leaf nodes
-- Andrew Page <ap13@sanger.ac.uk> Mon, 30 Mar 2015 14:17:00 +0000
gubbins (1.2.5~trusty1) trusty; urgency=low
* Block out SNPs from downstream recombinations
-- Andrew Page <ap13@sanger.ac.uk> Mon, 30 Mar 2015 14:17:00 +0000
gubbins (1.2.4~trusty1) trusty; urgency=low
* Python verion number in script
-- Andrew Page <ap13@sanger.ac.uk> Mon, 30 Mar 2015 14:17:00 +0000
gubbins (1.2.3~trusty1) trusty; urgency=low
* Eggs werent included in deb
-- Andrew Page <ap13@sanger.ac.uk> Mon, 30 Mar 2015 14:17:00 +0000
gubbins (1.2.2~trusty1) trusty; urgency=low
* Last sequence wasnt in array
-- Andrew Page <ap13@sanger.ac.uk> Mon, 30 Mar 2015 14:17:00 +0000
gubbins (1.2.1~trusty1) trusty; urgency=low
* Update VCF and EMBL output formats
-- Andrew Page <ap13@sanger.ac.uk> Mon, 30 Mar 2015 11:36:00 +0000
gubbins (1.2.0~trusty1) trusty; urgency=low
* Dont fill in parent bases with gaps from children
-- Andrew Page <ap13@sanger.ac.uk> Mon, 30 Mar 2015 10:16:00 +0000
gubbins (1.1.2~trusty1) trusty; urgency=low
* Fix GFF formatting and C warnings
-- Andrew Page <ap13@sanger.ac.uk> Fri, 23 Jan 2015 16:02:00 +0000
gubbins (1.1.1~trusty1) trusty; urgency=low
* Message to tell user theres a problem with outgroups not a clade
-- Andrew Page <ap13@sanger.ac.uk> Fri, 23 Jan 2015 16:02:00 +0000
gubbins (1.1.0~trusty1) trusty; urgency=low
* Allow for multiple outgroups
-- Andrew Page <ap13@sanger.ac.uk> Fri, 23 Jan 2015 15:05:00 +0000
gubbins (1.0.12~trusty1) trusty; urgency=low
* Remove internal labels from final tree
-- Andrew Page <ap13@sanger.ac.uk> Tue, 20 Jan 2015 09:03:00 +0000
gubbins (1.0.11~trusty1) trusty; urgency=low
* Test inputs contain variation
-- Andrew Page <ap13@sanger.ac.uk> Mon, 19 Jan 2015 09:01:00 +0000
gubbins (1.0.10~trusty1) trusty; urgency=low
* Upload failed on ubuntu
-- Andrew Page <ap13@sanger.ac.uk> Mon, 19 Jan 2015 09:01:00 +0000
gubbins (1.0.9~trusty1) trusty; urgency=low
* Remove cpu info and manually look for the flag
-- Andrew Page <ap13@sanger.ac.uk> Tue, 6 Jan 2015 14:09:00 +0000
gubbins (1.0.8~trusty1) trusty; urgency=low
* Limit the cpu info lookup to get around bug in ubuntu build
-- Andrew Page <ap13@sanger.ac.uk> Mon, 8 Dec 2014 12:58:00 +0000
gubbins (1.0.7~trusty1) trusty; urgency=low
* Update rho/theta calculation to blocks/snps outside recombinations
-- Andrew Page <ap13@sanger.ac.uk> Mon, 8 Dec 2014 12:58:00 +0000
gubbins (1.0.6~trusty1) trusty; urgency=low
* Drawer allow for variation tag
-- Andrew Page <ap13@sanger.ac.uk> Wed, 3 Dec 2014 11:32:00 +0000
gubbins (1.0.5~trusty1) trusty; urgency=low
* Fasttree executables with upper and lower case
-- Andrew Page <ap13@sanger.ac.uk> Wed, 19 Nov 2014 14:16:00 +0000
gubbins (1.0.4~trusty1) trusty; urgency=low
* Warning when number of threads changed for raxml
-- Andrew Page <ap13@sanger.ac.uk> Fri, 14 Nov 2014 14:16:00 +0000
gubbins (1.0.3~trusty1) trusty; urgency=low
* Dont use multiple threads for raxml if not requested
-- Andrew Page <ap13@sanger.ac.uk> Fri, 14 Nov 2014 14:16:00 +0000
gubbins (1.0.2~trusty1) trusty; urgency=low
* Allow for more convergence methods
-- Andrew Page <ap13@sanger.ac.uk> Tue, 14 Oct 2014 14:16:00 +0000
gubbins (1.0.1~trusty1) trusty; urgency=low
* Fixed unstable python test
-- Andrew Page <ap13@sanger.ac.uk> Tue, 14 Oct 2014 14:16:00 +0000
gubbins (1.0~trusty1) trusty; urgency=low
* Strict convergence option
-- Andrew Page <ap13@sanger.ac.uk> Tue, 14 Oct 2014 14:16:00 +0000
gubbins (0.6~trusty1) trusty; urgency=low
* Gubbins drawer can now use .embl file with recombination regions
-- Andrew Page <ap13@sanger.ac.uk> Tue, 9 Sep 2014 13:03:00 +0000
gubbins (0.5~trusty1) trusty; urgency=low
* Thread support for RAXML
-- Andrew Page <ap13@sanger.ac.uk> Tue, 9 Sep 2014 09:45:00 +0000
gubbins (0.4.1~trusty1) trusty; urgency=low
* Check for FastTree lowercase executable
-- Andrew Page <ap13@sanger.ac.uk> Mon, 8 Sep 2014 10:32:00 +0000
gubbins (0.4~trusty1) trusty; urgency=low
* Rename output files for pairwise comparison
-- Andrew Page <ap13@sanger.ac.uk> Fri, 5 Sep 2014 10:26:00 +0000
gubbins (0.3~trusty1) trusty; urgency=low
* Changes statistics file output
-- Andrew Page <ap13@sanger.ac.uk> Thu, 4 Sep 2014 17:07:00 +0000
gubbins (0.2~trusty1) trusty; urgency=low
* Rename final output files
-- Andrew Page <ap13@sanger.ac.uk> Mon, 1 Sep 2014 16:44:00 +0000
gubbins (0.1.11~trusty1) trusty; urgency=low
* Python remove internal node names if passed in as a starting tree
-- Andrew Page <ap13@sanger.ac.uk> Fri, 22 Aug 2014 16:44:00 +0000
gubbins (0.1.10~trusty1) trusty; urgency=low
* Python print list of excluded sequences to STDOUT by default
-- Andrew Page <ap13@sanger.ac.uk> Fri, 22 Aug 2014 14:44:00 +0000
gubbins (0.1.9~trusty1) trusty; urgency=low
* Python prints error messages for invalid sequence files and sends exit code 1
-- Andrew Page <ap13@sanger.ac.uk> Fri, 22 Aug 2014 10:37:00 +0000
gubbins (0.1.8~trusty1) trusty; urgency=low
* Python fastml exec fix
* Python check sequence names in tree
-- Andrew Page <ap13@sanger.ac.uk> Thu, 15 Aug 2014 16:32:00 +0000
gubbins (0.1.7~trusty2) trusty; urgency=low
* Package for trusty
* Move blocks further inwards
-- Andrew Page <ap13@sanger.ac.uk> Thu, 14 Aug 2014 09:56:00 +0000
gubbins (0.1.6) saucy; urgency=low
* Changed build depends
-- Aidan Delaney (Packaging Key) <aidan@ontologyengineering.org> Wed, 26 Jun 2014 14:46:07 +0000
gubbins (0.1.5) saucy; urgency=low
* Updated build system and removed some tests
-- Aidan Delaney (Packaging Key) <aidan@ontologyengineering.org> Wed, 25 Jun 2014 14:46:07 +0000
gubbins (0.1.4) saucy; urgency=low
* Updated Debian packages such that the build version is taken from Automake.
-- Aidan Delaney (Packaging Key) <aidan@ontologyengineering.org> Mon, 31 Mar 2014 14:46:07 +0000