| 2b0c0f3 | andrewjpage | 14 October 2014, 13:21:59 UTC | Merge pull request #112 from andrewjpage/converging_recombinations Converging recombinations | 14 October 2014, 13:21:59 UTC |
| 69a1900 | andrewjpage | 14 October 2014, 13:21:29 UTC | allow for strict convergence | 14 October 2014, 13:21:29 UTC |
| bee062c | andrewjpage | 14 October 2014, 09:22:20 UTC | get recombinations from embl file | 14 October 2014, 09:22:20 UTC |
| 1c10169 | andrewjpage | 14 October 2014, 08:17:18 UTC | Merge branch 'master' of github.com:sanger-pathogens/gubbins | 14 October 2014, 08:17:18 UTC |
| 7a929bd | andrewjpage | 24 September 2014, 08:22:03 UTC | Update README.md | 24 September 2014, 08:22:03 UTC |
| 23af202 | andrewjpage | 17 September 2014, 13:52:03 UTC | update install instructions | 17 September 2014, 13:52:03 UTC |
| 5488dab | andrewjpage | 09 September 2014, 14:59:42 UTC | homebrew | 09 September 2014, 14:59:42 UTC |
| 54d9985 | andrewjpage | 09 September 2014, 12:26:00 UTC | Merge pull request #111 from andrewjpage/master Gubbins drawer can use recombination embl file | 09 September 2014, 12:26:00 UTC |
| 78303dd | andrewjpage | 09 September 2014, 12:04:32 UTC | Gubbins drawer can use recombination embl file | 09 September 2014, 12:04:32 UTC |
| 5801e20 | andrewjpage | 09 September 2014, 11:40:47 UTC | Read version number from one place | 09 September 2014, 11:40:47 UTC |
| 62eda04 | andrewjpage | 09 September 2014, 08:51:56 UTC | Merge pull request #110 from andrewjpage/master thread support for raxml | 09 September 2014, 08:51:56 UTC |
| 059fe0c | andrewjpage | 09 September 2014, 08:49:41 UTC | thread support for raxml | 09 September 2014, 08:49:41 UTC |
| e5b92fb | andrewjpage | 08 September 2014, 09:42:18 UTC | Merge pull request #109 from andrewjpage/master Check for lowercase fasttree exec | 08 September 2014, 09:42:18 UTC |
| 572569c | andrewjpage | 08 September 2014, 09:41:30 UTC | Check for lowercase version of fast tree exec | 08 September 2014, 09:41:30 UTC |
| 3bf6aac | andrewjpage | 08 September 2014, 08:20:57 UTC | change email address and readme | 08 September 2014, 08:20:57 UTC |
| 6b496da | andrewjpage | 05 September 2014, 09:30:33 UTC | Merge pull request #108 from andrewjpage/pairwise_rename_files pairwise rename output files | 05 September 2014, 09:30:33 UTC |
| a9a73d8 | andrewjpage | 05 September 2014, 09:30:09 UTC | pairwise rename output files | 05 September 2014, 09:30:09 UTC |
| eafa6bd | andrewjpage | 04 September 2014, 16:09:30 UTC | Merge pull request #107 from andrewjpage/update_stats_headers Update stats headers | 04 September 2014, 16:09:30 UTC |
| 18feeee | andrewjpage | 04 September 2014, 16:08:16 UTC | Change stats output format and don't delete fastml tree | 04 September 2014, 16:08:16 UTC |
| 8732277 | andrewjpage | 02 September 2014, 13:08:29 UTC | move install to another file | 02 September 2014, 13:08:29 UTC |
| 155d08a | andrewjpage | 02 September 2014, 08:29:19 UTC | Merge pull request #106 from andrewjpage/catch_too_few_sequences Catch too few sequences | 02 September 2014, 08:29:19 UTC |
| 9151f5a | andrewjpage | 02 September 2014, 08:28:15 UTC | update to version 0.2 | 02 September 2014, 08:28:15 UTC |
| 1909cad | andrewjpage | 01 September 2014, 10:50:09 UTC | rename the output files to more meaningful names | 01 September 2014, 10:50:09 UTC |
| 97abcea | andrewjpage | 01 September 2014, 10:23:32 UTC | lookup tables for translating to final names plus prefix | 01 September 2014, 10:23:32 UTC |
| 1c3f3b1 | andrewjpage | 01 September 2014, 09:47:51 UTC | delete temp files from fastml | 01 September 2014, 09:47:51 UTC |
| 7404620 | andrewjpage | 27 August 2014, 12:34:38 UTC | fix uncommented tests | 27 August 2014, 12:34:38 UTC |
| ea26d93 | andrewjpage | 27 August 2014, 12:25:42 UTC | if you have less than 4 sequences you cant build a tree with raxml | 27 August 2014, 12:25:42 UTC |
| 7e6bd0d | andrewjpage | 22 August 2014, 15:49:59 UTC | Merge pull request #105 from andrewjpage/print_excluded_sequences version in configure | 22 August 2014, 15:49:59 UTC |
| fc07f88 | andrewjpage | 22 August 2014, 15:49:43 UTC | version in configure | 22 August 2014, 15:49:43 UTC |
| 4350943 | andrewjpage | 22 August 2014, 15:45:36 UTC | Merge pull request #104 from andrewjpage/print_excluded_sequences Support for bipartition trees as input | 22 August 2014, 15:45:36 UTC |
| c0ce86e | andrewjpage | 22 August 2014, 15:44:45 UTC | Support for bipartition trees as input | 22 August 2014, 15:44:45 UTC |
| cae13d8 | andrewjpage | 22 August 2014, 13:46:31 UTC | Merge pull request #103 from andrewjpage/print_excluded_sequences print list of excluded sequences | 22 August 2014, 13:46:31 UTC |
| 88103d2 | andrewjpage | 22 August 2014, 13:46:08 UTC | print list of excluded sequences | 22 August 2014, 13:46:08 UTC |
| 89faac9 | andrewjpage | 22 August 2014, 09:46:14 UTC | Merge pull request #102 from andrewjpage/master print errors for invalid input files | 22 August 2014, 09:46:14 UTC |
| 20268db | andrewjpage | 22 August 2014, 09:42:18 UTC | print errors for invalid input files | 22 August 2014, 09:42:18 UTC |
| e0f5498 | andrewjpage | 15 August 2014, 15:35:09 UTC | Merge pull request #101 from andrewjpage/fasttree_exec Fasttree exec | 15 August 2014, 15:35:09 UTC |
| 587f12c | andrewjpage | 15 August 2014, 15:34:50 UTC | version 0.1.8 | 15 August 2014, 15:34:50 UTC |
| 777524f | andrewjpage | 15 August 2014, 15:29:44 UTC | test for checking if names in fasta match tree | 15 August 2014, 15:29:44 UTC |
| 13991e5 | andrewjpage | 15 August 2014, 15:16:30 UTC | fasttree exec and taxon name check | 15 August 2014, 15:16:30 UTC |
| 7b601c8 | andrewjpage | 14 August 2014, 14:35:45 UTC | Merge pull request #100 from andrewjpage/master Build for trusty | 14 August 2014, 14:35:45 UTC |
| 4d56e0e | andrewjpage | 14 August 2014, 14:33:14 UTC | Merge branch 'master' of github.com:andrewjpage/gubbins | 14 August 2014, 14:33:14 UTC |
| 6c313b5 | andrewjpage | 14 August 2014, 14:32:59 UTC | update to trusty | 14 August 2014, 14:32:59 UTC |
| 901cd57 | andrewjpage | 14 August 2014, 13:32:13 UTC | build for trusty | 14 August 2014, 13:32:13 UTC |
| 1df26f6 | andrewjpage | 12 August 2014, 15:55:24 UTC | debian changes | 12 August 2014, 15:55:24 UTC |
| 1caef95 | andrewjpage | 12 August 2014, 12:39:40 UTC | Merge pull request #99 from andrewjpage/master Changes from Aidan Delaney | 12 August 2014, 12:39:40 UTC |
| 9a21644 | andrewjpage | 12 August 2014, 12:36:39 UTC | Revert "fix tests" fastml 2 gives slightly different results to fastml3 This reverts commit 0f590c525ed139ff6917d715049c139cc7872aa5. | 12 August 2014, 12:36:39 UTC |
| 0f590c5 | andrewjpage | 12 August 2014, 12:21:53 UTC | fix tests | 12 August 2014, 12:21:53 UTC |
| 2513b41 | andrewjpage | 07 August 2014, 15:53:57 UTC | changes | 07 August 2014, 15:53:57 UTC |
| 56b96a2 | andrewjpage | 07 August 2014, 09:46:53 UTC | Merge pull request #3 from AidanDelaney/master Packaging changes | 07 August 2014, 09:46:53 UTC |
| d8a7f28 | Aidan Delaney | 15 July 2014, 09:10:27 UTC | Linebreaks around bird-style code are necessary. | 15 July 2014, 09:10:27 UTC |
| 8d6e288 | Aidan Delaney | 15 July 2014, 09:09:51 UTC | Typo in build instructions | 15 July 2014, 09:09:51 UTC |
| 533d617 | Aidan Delaney | 15 July 2014, 09:08:19 UTC | Updated build instructions to account for new per-user requirements. | 15 July 2014, 09:08:19 UTC |
| 0ba36f3 | Aidan Delaney | 15 July 2014, 08:41:54 UTC | Fixed markdown formatting | 15 July 2014, 08:41:54 UTC |
| 1c19452 | Aidan Delaney | 15 July 2014, 08:36:36 UTC | Merge remote-tracking branch 'aidan/master' Conflicts: README.md install-userspace.sh | 15 July 2014, 08:36:36 UTC |
| a85ac9b | Jacqui Keane | 07 July 2014, 15:17:50 UTC | Updated install instructions and added a script to install application locally | 07 July 2014, 15:17:50 UTC |
| 0b76714 | Aidan Delaney | 06 July 2014, 20:38:53 UTC | Added an install script to allow people to install in their homedir. | 06 July 2014, 20:38:53 UTC |
| a5a92a2 | Aidan Delaney | 26 June 2014, 08:55:01 UTC | Updated README.md to include the INSTALL instructions. | 26 June 2014, 08:55:01 UTC |
| 2e24b7d | Aidan Delaney | 25 June 2014, 23:07:43 UTC | Updated the build depends, requiring a minor version bump. | 25 June 2014, 23:07:43 UTC |
| 33aa338 | Aidan Delaney | 25 June 2014, 22:26:27 UTC | Silly typo in Debian changelog | 25 June 2014, 22:26:27 UTC |
| 508e361 | Aidan Delaney | 25 June 2014, 22:23:33 UTC | Updated Debian changelog | 25 June 2014, 22:23:33 UTC |
| 7f506a6 | Aidan Delaney | 25 June 2014, 22:09:18 UTC | Remove fancy changelog.in in favour of vanilla changelog | 25 June 2014, 22:09:18 UTC |
| 0d95c61 | Aidan Delaney | 25 June 2014, 22:08:56 UTC | Remove RaXML test asserts | 25 June 2014, 22:08:56 UTC |
| 77dc717 | Aidan Delaney | 25 June 2014, 22:08:27 UTC | Ensure pkg-config is installed on VM | 25 June 2014, 22:08:27 UTC |
| 8aad266 | Aidan Delaney | 25 June 2014, 21:21:05 UTC | Minor bump to account for dependency on fastml2, rather than fastml3. | 25 June 2014, 21:21:05 UTC |
| 4c79171 | Aidan Delaney | 25 June 2014, 21:19:42 UTC | Forced use of correct packaging key | 25 June 2014, 21:19:42 UTC |
| d997fa3 | Aidan Delaney | 23 April 2014, 13:21:11 UTC | Updated debain package compat to something modern | 23 April 2014, 13:21:11 UTC |
| e761ef4 | Aidan Delaney | 16 April 2014, 10:45:12 UTC | Made external dependancies test look for binaries in $PATH rather than the previously bundled versions. | 16 April 2014, 10:45:12 UTC |
| f01a4f6 | Aidan Delaney | 16 April 2014, 10:44:38 UTC | Changed tar format as some of our test files go over the "traditional" 99 char length. | 16 April 2014, 10:44:38 UTC |
| 5aa912d | Aidan Delaney | 08 April 2014, 13:19:14 UTC | Integrated gubbins python bindings tests into the build. | 08 April 2014, 13:19:14 UTC |
| 145ae49 | Aidan Delaney | 08 April 2014, 11:46:17 UTC | Having removed the source of the external dependencies, we modify the python bindings such that they no longer use them. | 08 April 2014, 11:46:17 UTC |
| a836206 | Aidan Delaney | 08 April 2014, 10:11:44 UTC | External source dependencies are removed as they are now all available as .deb packages. | 08 April 2014, 10:11:44 UTC |
| 2f65344 | Aidan Delaney | 08 April 2014, 10:00:35 UTC | All of our external dependencies are now provided as Ubuntu packages. - the RaXML build uses the Makefile.generic which is the same as what is used by the Debian/Ubuntu packages. - fastml is now packaged in PPA for Ubuntu saucy, we'll expand this coverage later. | 08 April 2014, 10:00:35 UTC |
| 0e88f50 | Aidan Delaney | 07 April 2014, 12:42:20 UTC | Merge pull request #1 from zamaudio/deb_tweaks Made RaXML a recommended package, not a dependency, | 07 April 2014, 12:42:20 UTC |
| 4110d4d | Damien Zammit | 06 April 2014, 13:01:06 UTC | Made RaXML a recommended package, not a dependency, since standard-raxml will be built if it is not found. Also, some HPC facilities have customised builds of RaXML so it is not ideal to make the binary package a strict dependency. | 06 April 2014, 13:06:06 UTC |
| 6392f5d | Aidan Delaney | 01 April 2014, 10:35:29 UTC | Updated package dependancy list to include some of the python deps. | 01 April 2014, 10:35:29 UTC |
| 174d202 | Aidan Delaney | 31 March 2014, 19:26:53 UTC | Streamlining the Debiab/Ubuntu package release - Use @PACKAGE_*@ autoconf vars - generate some debian/* files | 31 March 2014, 19:26:53 UTC |
| 394eea2 | Aidan Delaney | 30 March 2014, 15:04:40 UTC | Added setup.py to the make | 30 March 2014, 15:04:40 UTC |
| 3c78f5a | Aidan Delaney | 25 March 2014, 07:14:06 UTC | Updated Debian build number to unclude a PPA string. | 25 March 2014, 07:14:06 UTC |
| 7b5ab17 | Aidan Delaney | 23 March 2014, 21:02:25 UTC | Use cp to /vagrant rather than scp - SCP likes to check the host key of our temporay VM, and won't connect if it has seen localhost:2222 before (which it probably has). | 23 March 2014, 21:02:25 UTC |
| e4e354b | Aidan Delaney | 23 March 2014, 20:20:32 UTC | Copy the .changes, .dsc and possibly modified .tar.gz to the build host. | 23 March 2014, 20:20:32 UTC |
| 0cc4894 | Aidan Delaney | 23 March 2014, 19:29:02 UTC | Build and configuration changes needed to build a gubbins .deb package. | 23 March 2014, 19:29:02 UTC |
| b83b2d6 | Aidan Delaney | 23 March 2014, 18:36:13 UTC | Make -lrt explicit for the tests (for POSIX timers). | 23 March 2014, 18:36:13 UTC |
| 989930c | Aidan Delaney | 23 March 2014, 18:17:46 UTC | libgubbins depends on libm, not just the gubbins binary. | 23 March 2014, 18:17:46 UTC |
| 1e83197 | Aidan Delaney | 23 March 2014, 17:31:29 UTC | Added minimial number of control files for a valid Debian package. | 23 March 2014, 17:31:29 UTC |
| a6f6836 | Aidan Delaney | 23 March 2014, 17:20:08 UTC | Added initial plumbing to get a configured Ubuntu 13.10 VM for release builds. | 23 March 2014, 17:20:08 UTC |
| c752294 | Aidan Delaney | 22 March 2014, 20:54:10 UTC | Modified the README to point at the INSTALL file for build instructions. | 22 March 2014, 20:54:10 UTC |
| a732c83 | Aidan Delaney | 22 March 2014, 20:25:17 UTC | Removed more autogenerated files and updated build documentation. | 22 March 2014, 20:25:17 UTC |
| 86c872c | Aidan Delaney | 22 March 2014, 20:14:31 UTC | Removed some autogenerated files. | 22 March 2014, 20:14:31 UTC |
| 975dd5a | Aidan Delaney | 22 March 2014, 20:01:26 UTC | Removed the external dependencies from the build - these are deps of the Python wrapper, not libgubbins.so. | 22 March 2014, 20:01:26 UTC |
| e87c889 | Aidan Delaney | 22 March 2014, 19:57:18 UTC | Moved definition of print_usage to before its first use. | 22 March 2014, 19:57:18 UTC |
| 6db20de | andrewjpage | 17 February 2014, 16:30:48 UTC | Merge pull request #98 from andrewjpage/stats_missing_snps Stats missing snps | 17 February 2014, 16:30:48 UTC |
| 7c2bf65 | andrewjpage | 17 February 2014, 16:27:19 UTC | if theres no recombination bases return the number of snps outside recombination | 17 February 2014, 16:27:19 UTC |
| 1b7298a | andrewjpage | 17 February 2014, 15:09:39 UTC | set total snps before looking up recombinations | 17 February 2014, 15:09:39 UTC |
| c993048 | andrewjpage | 29 January 2014, 09:35:28 UTC | Merge pull request #97 from andrewjpage/nosupport update no support option in fastml | 29 January 2014, 09:35:28 UTC |
| 33d98a6 | andrewjpage | 29 January 2014, 09:35:07 UTC | update no support option in fastml | 29 January 2014, 09:35:07 UTC |
| 390a5e0 | andrewjpage | 11 November 2013, 11:47:49 UTC | Merge pull request #96 from andrewjpage/master move blocks inwards | 11 November 2013, 11:47:49 UTC |
| 8a4036b | andrewjpage | 08 November 2013, 12:14:54 UTC | move blocks inwards | 08 November 2013, 12:14:54 UTC |
| 8288a89 | andrewjpage | 08 November 2013, 11:18:10 UTC | Merge pull request #95 from andrewjpage/master define is starting tree method as static | 08 November 2013, 11:18:10 UTC |
| 9e0c82a | andrewjpage | 08 November 2013, 11:17:35 UTC | define is starting tree method as static | 08 November 2013, 11:17:35 UTC |
| de10bba | andrewjpage | 19 September 2013, 08:48:38 UTC | Merge pull request #94 from andrewjpage/master starting tree needed to come from args | 19 September 2013, 08:48:38 UTC |
