| 67ab459 | Fernando Izquierdo | 28 August 2014, 19:15:46 UTC | added -p seed to scoring step | 28 August 2014, 19:15:46 UTC |
| c775530 | Fernando Izquierdo-Carrasco | 20 November 2013, 11:30:11 UTC | added ExaML link to the README | 20 November 2013, 11:30:11 UTC |
| ea6d668 | Fernando Izquierdo-Carrasco | 15 November 2013, 18:26:13 UTC | link to new tutorial | 15 November 2013, 18:26:13 UTC |
| bf3579a | Fernando Izquierdo-Carrasco | 14 November 2013, 15:26:38 UTC | fix call to states calculator in remote mode | 14 November 2013, 15:26:38 UTC |
| abc297d | Fernando Izquierdo-Carrasco | 13 November 2013, 16:24:29 UTC | fixed copy of partition file in standalone pipeline | 13 November 2013, 16:24:29 UTC |
| 22e58f2 | Fernando Izquierdo-Carrasco | 13 November 2013, 14:30:09 UTC | dont use exclude file in the PHLAWD example | 13 November 2013, 14:30:09 UTC |
| 60076fd | Fernando Izquierdo-Carrasco | 12 November 2013, 14:33:11 UTC | change defaults for parsi and bunch size | 12 November 2013, 14:33:11 UTC |
| 6846adf | Fernando Izquierdo-Carrasco | 07 November 2013, 13:55:21 UTC | fixed typo | 07 November 2013, 13:55:21 UTC |
| 8556f30 | Fernando Izquierdo-Carrasco | 07 November 2013, 13:48:59 UTC | User specifies type of data in the given alignment, default to DNA | 07 November 2013, 13:48:59 UTC |
| 67236fe | Fernando Izquierdo-Carrasco | 07 November 2013, 13:20:29 UTC | adapt evaluation to consider examl as a valid search file | 07 November 2013, 13:20:29 UTC |
| 4e024e4 | Fernando Izquierdo-Carrasco | 07 November 2013, 09:01:40 UTC | use pumper_installer as only installer | 07 November 2013, 09:01:40 UTC |
| deb1713 | Fernando Izquierdo | 06 November 2013, 17:17:48 UTC | Update README.md | 06 November 2013, 17:17:48 UTC |
| 054196a | Fernando Izquierdo | 06 November 2013, 17:15:38 UTC | Update README.md | 06 November 2013, 17:15:38 UTC |
| 38a1a5e | Fernando Izquierdo | 06 November 2013, 17:12:44 UTC | Update README.md | 06 November 2013, 17:12:44 UTC |
| 6f57c1b | Fernando Izquierdo-Carrasco | 06 November 2013, 13:06:19 UTC | use ExaML by default, otherwise Raxml-Light (standalone) | 06 November 2013, 13:06:19 UTC |
| 7760aa7 | Fernando Izquierdo-Carrasco | 06 November 2013, 12:07:37 UTC | added support of examl with partitioned files | 06 November 2013, 12:07:37 UTC |
| 650627a | Fernando Izquierdo-Carrasco | 06 November 2013, 09:59:08 UTC | added automatic binary file generation | 06 November 2013, 09:59:08 UTC |
| cccbf26 | Fernando Izquierdo-Carrasco | 06 November 2013, 09:01:38 UTC | basic integration of examl in standalone | 06 November 2013, 09:01:38 UTC |
| cdbc301 | Fernando Izquierdo-Carrasco | 05 November 2013, 18:15:21 UTC | fixed conflict | 05 November 2013, 18:15:21 UTC |
| d01932d | Fernando Izquierdo-Carrasco | 05 November 2013, 18:13:17 UTC | Automatic dload and installation of examl | 05 November 2013, 18:13:17 UTC |
| 82816b4 | Fernando Izquierdo-Carrasco | 05 November 2013, 15:03:39 UTC | clearer logs for remote submissions | 05 November 2013, 15:03:39 UTC |
| e8fd4b8 | Fernando Izquierdo-Carrasco | 05 November 2013, 14:26:06 UTC | refactoring iteration preparation | 05 November 2013, 14:26:06 UTC |
| e592f0a | Fernando Izquierdo-Carrasco | 05 November 2013, 12:32:39 UTC | removed duplication of code | 05 November 2013, 12:32:39 UTC |
| ebd505c | Fernando Izquierdo-Carrasco | 04 November 2013, 15:20:27 UTC | default value for partition file in remote mode | 04 November 2013, 15:20:27 UTC |
| c0a91a9 | Fernando Izquierdo-Carrasco | 04 November 2013, 14:22:34 UTC | another fix on update demo script | 04 November 2013, 14:22:34 UTC |
| 86aeacd | Fernando Izquierdo-Carrasco | 04 November 2013, 14:13:56 UTC | fix update demo script | 04 November 2013, 14:13:56 UTC |
| 4d568dd | Fernando Izquierdo-Carrasco | 04 November 2013, 14:03:11 UTC | avoid using symlinks | 04 November 2013, 14:03:11 UTC |
| 3541042 | Fernando Izquierdo-Carrasco | 04 November 2013, 13:56:20 UTC | added forgotten library | 04 November 2013, 13:56:20 UTC |
| e76d0e8 | Fernando Izquierdo-Carrasco | 04 November 2013, 13:36:39 UTC | fix curl call to from download github repos | 04 November 2013, 13:36:39 UTC |
| 14a6927 | Fernando Izquierdo-Carrasco | 31 October 2013, 16:31:23 UTC | Use curl instead of wget | 31 October 2013, 16:31:23 UTC |
| 8b84094 | Fernando Izquierdo-Carrasco | 31 October 2013, 15:30:45 UTC | fix partitions testing | 31 October 2013, 15:30:45 UTC |
| b41c32a | Fernando Izquierdo-Carrasco | 31 October 2013, 14:26:39 UTC | supress warning in results summarizer | 31 October 2013, 14:26:39 UTC |
| 0f6d91a | Fernando Izquierdo-Carrasco | 31 October 2013, 14:08:50 UTC | added update-from-scratch option, refactoring | 31 October 2013, 14:08:50 UTC |
| 913e25e | Fernando Izquierdo-Carrasco | 30 October 2013, 18:05:38 UTC | fix line | 30 October 2013, 18:05:38 UTC |
| 177f04e | Fernando Izquierdo-Carrasco | 30 October 2013, 18:03:07 UTC | organized library dependencies | 30 October 2013, 18:03:07 UTC |
| 7c6777d | Fernando Izquierdo-Carrasco | 30 October 2013, 17:48:40 UTC | even clearer logging functionality | 30 October 2013, 17:48:40 UTC |
| fa64cd1 | Fernando Izquierdo-Carrasco | 30 October 2013, 16:49:02 UTC | clearer log functionality | 30 October 2013, 16:49:02 UTC |
| a8f65ba | Fernando Izquierdo-Carrasco | 30 October 2013, 14:59:49 UTC | move log to base dir | 30 October 2013, 14:59:49 UTC |
| 2f0af9a | Fernando Izquierdo-Carrasco | 24 October 2013, 13:54:27 UTC | fix label for remote config file | 24 October 2013, 13:54:27 UTC |
| 84e0048 | Fernando Izquierdo-Carrasco | 24 October 2013, 13:20:12 UTC | fix rakefile | 24 October 2013, 13:20:12 UTC |
| 5e16019 | Fernando Izquierdo-Carrasco | 24 October 2013, 13:09:06 UTC | refactoring Rakefile | 24 October 2013, 13:09:06 UTC |
| 5c85374 | Fernando Izquierdo-Carrasco | 24 October 2013, 12:46:24 UTC | typo | 24 October 2013, 12:46:24 UTC |
| 1a30b8c | Fernando Izquierdo-Carrasco | 24 October 2013, 12:44:13 UTC | clean up generation of example | 24 October 2013, 12:44:13 UTC |
| a92c7fc | Fernando Izquierdo-Carrasco | 24 October 2013, 12:32:08 UTC | added rake task to test standalone + PHLAWD | 24 October 2013, 12:32:08 UTC |
| 3ece77f | Fernando Izquierdo-Carrasco | 24 October 2013, 12:24:09 UTC | fix generation of example runs | 24 October 2013, 12:24:09 UTC |
| e22b0df | Fernando Izquierdo-Carrasco | 24 October 2013, 11:54:49 UTC | adapted example for remote version | 24 October 2013, 11:54:49 UTC |
| 9298dc4 | Fernando Izquierdo-Carrasco | 24 October 2013, 11:19:26 UTC | remove references to remote version | 24 October 2013, 11:19:26 UTC |
| 8d2d1ca | Fernando Izquierdo-Carrasco | 24 October 2013, 08:57:12 UTC | more fixes on installation script | 24 October 2013, 08:57:12 UTC |
| bad444b | Fernando Izquierdo-Carrasco | 24 October 2013, 08:38:08 UTC | fix installation argument | 24 October 2013, 08:38:08 UTC |
| 63ed1a4 | Fernando Izquierdo-Carrasco | 24 October 2013, 08:32:04 UTC | fixed gem dependencies | 24 October 2013, 08:32:04 UTC |
| e66f97d | Fernando Izquierdo-Carrasco | 24 October 2013, 08:28:38 UTC | merge installation scripts | 24 October 2013, 08:28:38 UTC |
| a0273b6 | Fernando Izquierdo-Carrasco | 24 October 2013, 07:54:34 UTC | fixed requirements for standalone installation | 24 October 2013, 07:54:34 UTC |
| 884cc74 | Fernando Izquierdo-Carrasco | 23 October 2013, 15:24:36 UTC | copy only the relevant libraries for each installation version | 23 October 2013, 15:24:36 UTC |
| d94bf5c | Fernando Izquierdo-Carrasco | 23 October 2013, 15:11:17 UTC | separation of installation of remote and standalone versions | 23 October 2013, 15:11:17 UTC |
| 7a3ce52 | Fernando Izquierdo-Carrasco | 23 October 2013, 13:55:45 UTC | default installation as standalone | 23 October 2013, 13:55:45 UTC |
| 0929f3e | Fernando Izquierdo-Carrasco | 23 October 2013, 13:22:15 UTC | eliminated external ruby gem dependencies for standalone version | 23 October 2013, 13:22:15 UTC |
| 21cb578 | Fernando Izquierdo-Carrasco | 23 October 2013, 11:52:12 UTC | more generic version check | 23 October 2013, 11:52:12 UTC |
| d13412f | Fernando Izquierdo-Carrasco | 23 October 2013, 10:23:21 UTC | added a rvm installer | 23 October 2013, 10:23:21 UTC |
| a215e22 | Fernando Izquierdo | 22 October 2013, 18:58:28 UTC | better msg for default standalone mode | 22 October 2013, 18:58:28 UTC |
| f1e2818 | Fernando Izquierdo | 22 October 2013, 18:52:50 UTC | Use always the locally installed raxml-pumper binaries | 22 October 2013, 18:52:50 UTC |
| af7f706 | Fernando Izquierdo | 22 October 2013, 18:06:57 UTC | include pumper executables installation in the install_dependencies script | 22 October 2013, 18:06:57 UTC |
| 24dcce5 | Fernando Izquierdo | 22 October 2013, 17:36:56 UTC | deleted fake-phy option | 22 October 2013, 17:36:56 UTC |
| 3d778cd | Fernando Izquierdo | 22 October 2013, 17:19:55 UTC | automated download and installation of raxml-family source | 22 October 2013, 17:19:55 UTC |
| 8dc8e2e | Fernando Izquierdo | 22 October 2013, 10:40:22 UTC | automated ruby version checks and dependencies installation | 22 October 2013, 10:40:22 UTC |
| 64f3d63 | Fernando Izquierdo-Carrasco | 17 September 2013, 12:11:44 UTC | added script to evaluate per-partition support | 17 September 2013, 12:11:44 UTC |
| 105c497 | Fernando Izquierdo-Carrasco | 13 August 2013, 09:15:48 UTC | update url | 13 August 2013, 09:15:48 UTC |
| f50cbca | Fernando Izquierdo-Carrasco | 13 August 2013, 09:12:04 UTC | links in README | 13 August 2013, 09:12:04 UTC |
| 00a2495 | Fernando Izquierdo-Carrasco | 12 August 2013, 16:00:59 UTC | license note | 12 August 2013, 16:00:59 UTC |
| 7776540 | Fernando Izquierdo-Carrasco | 12 August 2013, 15:58:26 UTC | smaller title | 12 August 2013, 15:58:26 UTC |
| f5be6bb | Fernando Izquierdo-Carrasco | 12 August 2013, 15:57:14 UTC | Updated README | 12 August 2013, 15:57:14 UTC |
| 78a017a | Fernando Izquierdo-Carrasco | 12 August 2013, 15:43:29 UTC | Replace names by PUMPER | 12 August 2013, 15:43:29 UTC |
| aedea96 | Fernando Izquierdo-Carrasco | 09 July 2013, 10:06:01 UTC | Use only last info file to summarize total search time | 09 July 2013, 10:06:01 UTC |
| dfa0b3d | Fernando Izquierdo-Carrasco | 04 July 2013, 09:42:52 UTC | change project name | 04 July 2013, 09:42:52 UTC |
| 736f0a2 | Fernando Izquierdo-Carrasco | 07 June 2013, 12:25:44 UTC | log iteration and gene name in each phlawd instance run | 07 June 2013, 12:25:44 UTC |
| f4938a0 | Fernando Izquierdo-Carrasco | 03 June 2013, 14:06:55 UTC | small fix | 03 June 2013, 14:06:55 UTC |
| 2b962fd | Fernando Izquierdo-Carrasco | 03 June 2013, 12:42:42 UTC | save used mapping of IDs and taxa names for each supermatrix built | 03 June 2013, 12:42:42 UTC |
| 116a889 | Fernando Izquierdo-Carrasco | 03 June 2013, 10:05:32 UTC | use ncbi numeric ids to identify taxa | 03 June 2013, 10:05:32 UTC |
| 198416e | Fernando Izquierdo-Carrasco | 29 May 2013, 12:21:08 UTC | specs for iteration_finish not ready yet | 29 May 2013, 12:21:08 UTC |
| 8c8e2aa | Fernando Izquierdo-Carrasco | 29 May 2013, 09:09:57 UTC | remote connection specs | 29 May 2013, 09:09:57 UTC |
| 2eb9552 | Fernando Izquierdo-Carrasco | 28 May 2013, 15:05:47 UTC | re-use test data from single project | 28 May 2013, 15:05:47 UTC |
| ccd7092 | Fernando Izquierdo-Carrasco | 28 May 2013, 14:47:04 UTC | fix check for collection of trees at the end of iteration | 28 May 2013, 14:47:04 UTC |
| ee10d72 | Fernando Izquierdo-Carrasco | 28 May 2013, 14:02:06 UTC | added specs for project results | 28 May 2013, 14:02:06 UTC |
| 1f94974 | Fernando Izquierdo-Carrasco | 28 May 2013, 12:51:05 UTC | added specs for the configuration of a remote connection | 28 May 2013, 12:51:05 UTC |
| 0483c73 | Fernando Izquierdo-Carrasco | 27 May 2013, 17:32:52 UTC | continue if a single phlawd gene update fails | 27 May 2013, 17:32:52 UTC |
| ea85809 | Fernando Izquierdo-Carrasco | 23 May 2013, 14:11:40 UTC | ensure fasta file exists | 23 May 2013, 14:11:40 UTC |
| beec141 | Fernando Izquierdo-Carrasco | 22 May 2013, 23:24:16 UTC | retry 5 times for failed ssh/scp network operations | 22 May 2013, 23:24:16 UTC |
| 54cec81 | Fernando Izquierdo-Carrasco | 17 May 2013, 16:22:40 UTC | removed commented code | 17 May 2013, 16:22:40 UTC |
| 6172ab2 | Fernando Izquierdo-Carrasco | 17 May 2013, 15:55:59 UTC | annotate a rebuild as done after a supermeatrix has been built | 17 May 2013, 15:55:59 UTC |
| 695ba5e | Fernando Izquierdo-Carrasco | 17 May 2013, 13:02:59 UTC | silence logs run under cron jobs | 17 May 2013, 13:02:59 UTC |
| 5fbab94 | Fernando Izquierdo-Carrasco | 17 May 2013, 12:45:28 UTC | refactor next alignment resolution | 17 May 2013, 12:45:28 UTC |
| 577898a | Fernando Izquierdo-Carrasco | 17 May 2013, 12:04:09 UTC | remove unused code and unrequired system call | 17 May 2013, 12:04:09 UTC |
| 24e674f | Fernando Izquierdo-Carrasco | 16 May 2013, 13:39:03 UTC | removed unused code | 16 May 2013, 13:39:03 UTC |
| 4d8fd0c | Fernando Izquierdo-Carrasco | 15 May 2013, 17:29:23 UTC | automatic merge of new phylip files into a supermatrix for next iter | 15 May 2013, 17:29:23 UTC |
| 5e73709 | Fernando Izquierdo-Carrasco | 15 May 2013, 15:32:35 UTC | independendt run updates for each phlawd instance, auto merge of the phylips pending | 15 May 2013, 15:32:35 UTC |
| 5019e49 | Fernando Izquierdo-Carrasco | 15 May 2013, 11:09:12 UTC | report stats on the number of search steps(iterations) at each pipeline iteration | 15 May 2013, 11:09:12 UTC |
| 0ac5927 | Fernando Izquierdo-Carrasco | 14 May 2013, 20:24:26 UTC | generate db.update file automatically | 14 May 2013, 20:24:26 UTC |
| ff7713a | Fernando Izquierdo-Carrasco | 14 May 2013, 15:26:07 UTC | find common Genbank DB path of all phlawd instances | 14 May 2013, 15:26:07 UTC |
| 7f9d29b | Fernando Izquierdo-Carrasco | 14 May 2013, 14:43:38 UTC | script to identify the need for an alignment extensions can consider several gene regions | 14 May 2013, 14:43:38 UTC |
| 4ef8980 | Fernando Izquierdo-Carrasco | 14 May 2013, 14:38:27 UTC | parse user input from each phlawd runfile | 14 May 2013, 14:38:27 UTC |
| bd9005e | Fernando Izquierdo-Carrasco | 14 May 2013, 13:59:01 UTC | rename test gene to comply with case-sensitive matching | 14 May 2013, 13:59:01 UTC |
