| 350d1ed | Aaron Petkau | 06 September 2016, 22:10:20 UTC | Updated readme to point to newer location | 06 September 2016, 22:10:20 UTC |
| e554b40 | Aaron Petkau | 16 November 2015, 23:08:52 UTC | Merge branch 'release-0.3' | 16 November 2015, 23:08:52 UTC |
| a8622a2 | Cameron | 16 November 2015, 22:08:27 UTC | Merge branch 'feature/update-snvphyl-w-freebayes' into 'release-0.3' Feature/update snvphyl w freebayes This completes all the changes for releasing SNVPhyl 0.3. That is, the documentation and virtual machines are updated. I'm mostly looking for a review of documentation changes here. I have them being rendered on my machine at http://jupiter:8001/. This is being merged into branch `release-0.3`. I plan to merge this branch into master and development right afterwards. See merge request !38 | 16 November 2015, 22:08:27 UTC |
| 158ec74 | Aaron Petkau | 16 November 2015, 19:17:04 UTC | Correcting usage | 16 November 2015, 19:17:04 UTC |
| f83b100 | Aaron Petkau | 16 November 2015, 19:14:30 UTC | Fixed Galaxy instructions info | 16 November 2015, 19:14:30 UTC |
| 3f47f2a | Aaron Petkau | 16 November 2015, 13:51:48 UTC | Merge branch 'feature/update-snvphyl-w-freebayes' of gitlab-irida.corefacility.ca:analysis-pipelines/snvphyl-galaxy into feature/update-snvphyl-w-freebayes | 16 November 2015, 13:51:48 UTC |
| 07b315e | Aaron Petkau | 15 November 2015, 23:19:07 UTC | Corrected mistake with snvphyl-galaxy docker | 15 November 2015, 23:19:07 UTC |
| 35e9cc8 | Aaron Petkau | 15 November 2015, 23:10:47 UTC | Updated docker command | 15 November 2015, 23:10:47 UTC |
| 30d99a4 | Aaron Petkau | 15 November 2015, 22:19:40 UTC | Remove extra directories from Docker image | 15 November 2015, 22:19:40 UTC |
| 91f8e9e | Aaron Petkau | 15 November 2015, 22:07:36 UTC | Updated virtual machine for 0.3 | 15 November 2015, 22:07:36 UTC |
| 671b952 | Aaron Petkau | 13 November 2015, 21:59:41 UTC | Updated Dockerfile | 13 November 2015, 21:59:41 UTC |
| a5f171d | Aaron Petkau | 13 November 2015, 21:56:57 UTC | Updated repository dependencies and versions document | 13 November 2015, 21:56:57 UTC |
| 19b8fa5 | Aaron Petkau | 13 November 2015, 21:45:52 UTC | Updating Galaxy install guide for 0.3 | 13 November 2015, 21:45:52 UTC |
| 853e2d9 | Aaron Petkau | 13 November 2015, 21:10:07 UTC | Turn off indel calling | 13 November 2015, 21:10:07 UTC |
| 6e320d7 | Aaron Petkau | 13 November 2015, 20:16:12 UTC | Merged release-0.3 | 13 November 2015, 20:16:12 UTC |
| b75c017 | Philip Mabon | 13 November 2015, 17:14:21 UTC | Merge branch 'feature/release-versions' into 'release-0.3' Feature/release versions Hey, This adds documentation for my plan on how to handle upgrades to SNVPhyl. In particular, it attempts to address issue #45 where the `suite_snvphyl` and `package_snvphyl` repositories must be kept separate for each version number. It also defines a model for versions for `package_snvphyl`. That is, there will be a repository `package_snvphyl_1_5` corresponding to a version `1.5`. Any tools depending on this version will have a version number `1.5.x`. Where `x` can be modified to make small changes that don't update the dependency version. Moving to `package_snvphyl_1_6` will force all tools to update to version `1.6.x`. You can construct the docs with `mkdocs serve`, or review them at http://jupiter:8001/developer/upgrading/. This is going to branch `release-0.3`. Once I've released SNVPhyl 0.3, I'll merge this back into development. See merge request !37 | 13 November 2015, 17:14:21 UTC |
| 4371103 | Aaron Petkau | 12 November 2015, 17:53:16 UTC | Misspelled target | 12 November 2015, 17:53:16 UTC |
| 820fd92 | Aaron Petkau | 12 November 2015, 16:48:35 UTC | wrong link | 12 November 2015, 16:48:35 UTC |
| 2690897 | Aaron Petkau | 12 November 2015, 16:38:51 UTC | Added summary for upgrading instructions | 12 November 2015, 16:41:23 UTC |
| c561f83 | Aaron Petkau | 12 November 2015, 16:08:00 UTC | Wrote document for upgrading snvphyl | 12 November 2015, 16:08:00 UTC |
| 41c6d1f | Aaron Petkau | 10 November 2015, 18:29:19 UTC | Updated tool versions for 0.3 | 10 November 2015, 18:29:19 UTC |
| 1efb837 | Aaron Petkau | 10 November 2015, 18:00:50 UTC | Updated version of snvphyl installed | 10 November 2015, 18:00:50 UTC |
| 20daa6e | Aaron Petkau | 10 November 2015, 17:34:23 UTC | Updating version numbers of each package for better release tracking | 10 November 2015, 17:34:23 UTC |
| 86bc9c8 | Cameron | 06 November 2015, 20:19:51 UTC | Merge branch 'fix/snvphyl-0.2-docs' into 'release-0.3' Fix/snvphyl 0.2 docs This updates documentation for SNVPhyl version 0.2 to change the repository from `suite_snvphyl` to `suite_snvphyl_0_2_0`. This merges to a branch `release-0.3` since I wanted it in my 0.3 release. After merging this in, can you also manually merge/push to development. Then, delete this branch `fix/snvphyl-0.2-docs` by hand with: ``` git push origin --delete fix/snvphyl-0.2-docs ``` Thanks. See merge request !33 | 06 November 2015, 20:19:51 UTC |
| 5a5a1ee | Aaron Petkau | 05 November 2015, 15:10:43 UTC | Wording | 05 November 2015, 15:10:43 UTC |
| caefa60 | Aaron Petkau | 04 November 2015, 20:34:11 UTC | Updated repo dependencies to 0.2.0 | 04 November 2015, 20:34:11 UTC |
| 42a4fc7 | Aaron Petkau | 04 November 2015, 20:31:28 UTC | Updating to suite_snvphyl_0_2_0 | 04 November 2015, 20:31:28 UTC |
| 6215a78 | Aaron Petkau | 29 October 2015, 14:29:57 UTC | Updated docker for snvphyl 0.3 | 29 October 2015, 14:29:57 UTC |
| 4d52489 | Aaron Petkau | 27 October 2015, 20:59:42 UTC | Changing instances of 0.2 to 0.3 | 27 October 2015, 20:59:42 UTC |
| d3b02db | Aaron Petkau | 27 October 2015, 20:33:29 UTC | Updated links/verion | 27 October 2015, 20:33:29 UTC |
| 880864a | Aaron Petkau | 27 October 2015, 20:09:25 UTC | Updated workflow in docs and script for building VM | 27 October 2015, 20:09:25 UTC |
| 03f72d1 | Aaron Petkau | 27 October 2015, 18:36:28 UTC | Updated SNVPhyl to 0.3 and modified repository dependencies | 27 October 2015, 18:36:28 UTC |
| 72100df | Aaron Petkau | 27 October 2015, 14:38:55 UTC | Updated invalid positions workflow to 0.3 | 27 October 2015, 14:40:33 UTC |
| 6f5c44e | Aaron Petkau | 26 October 2015, 21:23:30 UTC | Updating to initial 0.3 workflow | 27 October 2015, 14:40:33 UTC |
| 0292943 | Aaron Petkau | 26 October 2015, 19:52:28 UTC | Added script to check for differences in toolshed | 27 October 2015, 14:40:33 UTC |
| b979e30 | Aaron Petkau | 26 October 2015, 19:46:26 UTC | Re-wording | 27 October 2015, 14:40:33 UTC |
| 3aa46d9 | Aaron Petkau | 26 October 2015, 16:34:08 UTC | Updated information on how to upload tools to a toolshed | 27 October 2015, 14:40:33 UTC |
| 84aaef3 | Aaron Petkau | 26 October 2015, 16:26:22 UTC | Adding section on snvphyl versions | 27 October 2015, 14:40:33 UTC |
| 36aad3d | Aaron Petkau | 27 October 2015, 14:18:35 UTC | Merge branch 'fix_smalt_sort' into 'development' typo, referencing wrong samtools version my mistake. Should work now. See merge request !30 | 27 October 2015, 14:18:35 UTC |
| dd74f6d | Takadonet | 27 October 2015, 14:05:48 UTC | typo, referencing wrong samtools version | 27 October 2015, 14:05:48 UTC |
| 8c84367 | Philip Mabon | 26 October 2015, 15:52:03 UTC | Merge branch 'fix/update-irida-url' into 'development' Fix/update irida url Fix up any URLs in repository from `http` to `https`, and from `irida.corefacility.ca/gitlab` to `irida.corefacility.ca/`. See merge request !29 | 26 October 2015, 15:52:03 UTC |
| 557f9b0 | Aaron Petkau | 26 October 2015, 15:45:23 UTC | Increment version number for snvphyl-tools | 26 October 2015, 15:45:23 UTC |
| 2a6c0b2 | Aaron Petkau | 26 October 2015, 15:35:49 UTC | Updated version number for package_snvphyl | 26 October 2015, 15:35:49 UTC |
| deb6b98 | Aaron Petkau | 26 October 2015, 15:03:32 UTC | Removed gitlab/ from few remaining URLs | 26 October 2015, 15:03:32 UTC |
| 6bb8c40 | Aaron Petkau | 26 October 2015, 14:49:18 UTC | Changed gitlab url for snvphyl git | 26 October 2015, 15:00:21 UTC |
| 881d62c | Aaron Petkau | 26 October 2015, 14:37:04 UTC | Merge branch 'multiple_thread_smalt_samtools' into 'development' Multiple thread smalt samtools Forgot to tell Jen to add multiple threading to samtools sort after we generated a bam file from smalt map. It uses the environment variable passed by Galaxy called '$GALAXY_SLOTS' . Galaxy populate it based on the number of cores indicated in job_conf.xml. All tools for the smalt mapper now is multiple threaded and runs fast as hell now! See merge request !28 | 26 October 2015, 14:37:04 UTC |
| ef66859 | Takadonet | 23 October 2015, 20:57:32 UTC | ensure that samtool sort will work outside of galaxy | 23 October 2015, 20:57:32 UTC |
| d9a34ad | Takadonet | 23 October 2015, 14:34:27 UTC | updated the smalt version number as well | 23 October 2015, 14:34:27 UTC |
| 11a310e | Takadonet | 23 October 2015, 14:33:00 UTC | forgot to add multiple samtools sort after creating a bam file from smalt map. It uses the environement variable GALAXY_SLOTS provided by galaxy | 23 October 2015, 14:33:00 UTC |
| 6c41c0d | Cameron | 16 October 2015, 19:47:47 UTC | Merge branch 'docs/update-main-screenshot' into 'development' Updated main screenshot This updates the main screenshot to a circular tree from the **Listeria** example that was just merged in. See merge request !26 | 16 October 2015, 19:47:47 UTC |
| e14a9e6 | Aaron Petkau | 16 October 2015, 19:44:44 UTC | Merge branch 'fix_seqtknml' into 'development' Fix seqtknml issues Fixed up the following issues from Aaron previous merge request: Move stdout into it's own log file with what coverage value we are downsampling too. Add usage statement Changes scp to cp Added test for actually downsampling. See merge request !24 | 16 October 2015, 19:44:44 UTC |
| 612d4ba | Takadonet | 15 October 2015, 17:07:37 UTC | check the error code coming for seqtk and dieding if a non zero code is found. Added documenatation for --type | 15 October 2015, 17:07:37 UTC |
| 756967a | Aaron Petkau | 15 October 2015, 16:23:53 UTC | Merge branch 'replace_freebayes' into 'development' Replace freebayes Switch over from using our old freebayes v 0.9 to publicly available freebayes v .9.20 from devteam on external public toolshed. See merge request !25 | 15 October 2015, 16:23:53 UTC |
| 23d7dcb | Aaron Petkau | 15 October 2015, 16:21:45 UTC | Updated main screenshot | 15 October 2015, 16:21:45 UTC |
| 6820052 | Takadonet | 15 October 2015, 16:11:27 UTC | removed freebayes from tools-to-install.txt . Was removed in other seqtknml branch | 15 October 2015, 16:11:27 UTC |
| 9d17879 | Takadonet | 15 October 2015, 16:09:40 UTC | using now File::Copy instead of just unix cp directly. Added more die statement if missing information. Convert one liner to a pure perl function. No big speed differences... Updated test log files to reflect fixes in typos | 15 October 2015, 16:09:40 UTC |
| 9150c01 | Aaron Petkau | 15 October 2015, 15:54:29 UTC | Merge branch 'feature/update-examples' into 'development' Completion of Listeria example for SNVPhyl documentation. See merge request !22 | 15 October 2015, 15:54:29 UTC |
| 91200ff | csieffert | 15 October 2015, 15:33:42 UTC | Changed name for mpileup variant caller | 15 October 2015, 15:33:42 UTC |
| 6bd62e4 | csieffert | 15 October 2015, 15:09:57 UTC | Remove ecoli header in mkdocs.yml for this branch | 15 October 2015, 15:09:57 UTC |
| 79e245c | csieffert | 15 October 2015, 14:45:00 UTC | Merging updated development branch into current branch | 15 October 2015, 14:45:00 UTC |
| 3e88aa9 | csieffert | 15 October 2015, 13:17:04 UTC | Implemented recommended changes from the merge request | 15 October 2015, 13:17:04 UTC |
| 2f98dec | Takadonet | 14 October 2015, 20:27:48 UTC | added die statement if non zero exit code | 14 October 2015, 20:27:48 UTC |
| c0ac782 | Takadonet | 14 October 2015, 19:37:52 UTC | forgot to kill this repo! | 14 October 2015, 19:37:52 UTC |
| 4a72a6d | Takadonet | 14 October 2015, 16:53:20 UTC | added the new verison of freebayes and its dependencies. Made them all separate. Hate that we have 3 version of samtools... But no choice. Planning to get them to change to at least 0.1.19 | 14 October 2015, 16:53:20 UTC |
| 51431c6 | Takadonet | 14 October 2015, 16:39:57 UTC | now using the public freebayes with version 0.9.20 instead of our old version of 0.9.9 | 14 October 2015, 16:39:57 UTC |
| 57ffccc | Takadonet | 14 October 2015, 16:39:21 UTC | removed reference to our local old freebayes version from the repo | 14 October 2015, 16:39:21 UTC |
| 1df073c | Takadonet | 13 October 2015, 20:47:19 UTC | added usage statement, print out all info to log. Added which coverage value we are downsampling to. | 13 October 2015, 20:47:19 UTC |
| b028358 | Takadonet | 13 October 2015, 18:00:39 UTC | fixed 'scp to 'cp' | 13 October 2015, 18:00:39 UTC |
| 0054082 | Takadonet | 13 October 2015, 17:56:52 UTC | added new test where you actually have two downsample | 13 October 2015, 17:56:52 UTC |
| 612e3c3 | csieffert | 13 October 2015, 16:33:13 UTC | Note on the state of filtered density statistic | 13 October 2015, 16:33:13 UTC |
| 8e8136f | csieffert | 13 October 2015, 15:31:12 UTC | Implement merge request changes, remove duplicate list value, expand interpretation explanation, remove uncesseary line in step 5 | 13 October 2015, 15:31:12 UTC |
| ac44e46 | Franklin Bristow | 09 October 2015, 16:47:01 UTC | Merge branch 'feature/asm-challenge' into 'development' Added reference to ASM NGS challenge This adds a reference to the results for the ASM NGS Challenge for SNVPhyl. See merge request !23 | 09 October 2015, 16:47:01 UTC |
| ca15abf | Aaron Petkau | 09 October 2015, 16:21:57 UTC | Fixed typos | 09 October 2015, 16:21:57 UTC |
| 97c4642 | Aaron Petkau | 09 October 2015, 16:08:51 UTC | Added reference to ASM NGS challenge | 09 October 2015, 16:08:51 UTC |
| 36188b0 | csieffert | 06 October 2015, 20:07:47 UTC | Adding additional screenshots. | 06 October 2015, 20:07:47 UTC |
| fa912e1 | csieffert | 06 October 2015, 20:02:57 UTC | Small grammar changes plus new images describing reference name for invalid positions file. | 06 October 2015, 20:02:57 UTC |
| 8b3e82c | csieffert | 06 October 2015, 19:23:56 UTC | Added tree image into document | 06 October 2015, 19:23:56 UTC |
| af2ce68 | csieffert | 05 October 2015, 16:49:37 UTC | Bolding appropriate file names, edited images to make more human readable, small grammar changes. | 05 October 2015, 16:49:37 UTC |
| 854da15 | csieffert | 05 October 2015, 15:53:18 UTC | Fixed link, bolded invalid-positions.bed filename, re-numbered steps | 05 October 2015, 15:53:18 UTC |
| dec4837 | Aaron Petkau | 02 October 2015, 20:14:24 UTC | Merge branch 'development' | 02 October 2015, 20:14:24 UTC |
| c914b7d | Aaron Petkau | 02 October 2015, 20:13:58 UTC | Merge branch 'development' of github.com:apetkau/snvphyl-galaxy into development | 02 October 2015, 20:13:58 UTC |
| beb8010 | Aaron Petkau | 02 October 2015, 20:06:48 UTC | Merge branch 'development' | 02 October 2015, 20:06:48 UTC |
| dc530d5 | Philip Mabon | 02 October 2015, 19:08:45 UTC | Merge branch 'feature/update-tool-dependencies' into 'development' Feature/update tool dependencies This updates the dependencies and adds additional tools for SNVPhyl, as well as a method to install and update in a toolshed. To install to a new toolshed, make sure the following categories are available: * Sequence Analysis * Text Manipulation * Tool Dependency Packages * Variant Analysis Then, install anything in the directory `tools/capsules`, then run: ``` ./scripts/run_planemo_for_tools.sh shed_create --shed_target http://localhost:9010 --shed_key ea809d4dfc353fa1c2050d9c256747ba -m "commit" ``` This runs planemo on all the tools (in the proper order). The default owner for all tools is `nml`, but you can pass any owner you want, along with any other parameters to planemo. To update tools, just run: ``` ./scripts/run_planemo_for_tools.sh shed_update --shed_target http://localhost:9010 --shed_key ea809d4dfc353fa1c2050d9c256747ba -m "commit" ``` This will update any tools (ignoring those with no differences) and finally update `suite_snvphyl` if any changes have been made. See merge request !19 | 02 October 2015, 19:08:45 UTC |
| 74ec079 | Takadonet | 30 September 2015, 16:24:10 UTC | Merge branch 'development' of http://irida.corefacility.ca/gitlab/analysis-pipelines/snvphyl-galaxy into development | 30 September 2015, 16:24:10 UTC |
| 6a5a84c | Takadonet | 30 September 2015, 16:21:50 UTC | Mariam changes for the snvphyl_reporter. Could not resolve her merge request because of conflicts and also not able to access her repo to fix them. So just commiting directly | 30 September 2015, 16:21:50 UTC |
| ff935bd | Aaron Petkau | 27 September 2015, 13:35:51 UTC | Added contact info | 27 September 2015, 13:35:51 UTC |
| 81743b4 | csieffert | 25 September 2015, 18:51:49 UTC | Grammar changes | 25 September 2015, 18:51:49 UTC |
| bb80262 | csieffert | 25 September 2015, 18:35:26 UTC | Quick fix to mkdocs.yml | 25 September 2015, 18:35:26 UTC |
| 4205d17 | csieffert | 25 September 2015, 16:39:24 UTC | Resolving xconflicts | 25 September 2015, 16:39:24 UTC |
| e39fd6a | csieffert | 25 September 2015, 16:32:40 UTC | Completion of Listeria example for SNVPhyl documentation. | 25 September 2015, 16:32:40 UTC |
| 52c42cf | Franklin Bristow | 22 September 2015, 12:58:10 UTC | Merge branch 'feature/update-documentation' into 'development' Feature/update documentation This updates the SNVPhyl documentation to include installation instructions, fixes the front page, as well as usage instructions. You can view the docs using `mkdocs`, which can be installed and run with: ``` pip install mkdocs cd snvphyl-galaxy/ mkdocs serve ``` The are also running on http://jupiter:8000 if you want to review. @philip.mabon and @csieffert you may want to see this as well. There's still a few more sections to add but this is the bulk of it. See merge request !21 | 22 September 2015, 12:58:10 UTC |
| 8461109 | Aaron Petkau | 22 September 2015, 02:46:50 UTC | Updated layout | 22 September 2015, 02:46:50 UTC |
| aaa8862 | Aaron Petkau | 22 September 2015, 02:33:55 UTC | Updating with extra dependencies | 22 September 2015, 02:33:55 UTC |
| 1a31ad0 | Aaron Petkau | 22 September 2015, 02:27:35 UTC | Added list of dependencies | 22 September 2015, 02:28:53 UTC |
| e3ad2ea | Aaron Petkau | 22 September 2015, 02:00:08 UTC | Updated virtual machine to remove older snvphyl workflow | 22 September 2015, 02:08:09 UTC |
| 8a0c09d | Aaron Petkau | 21 September 2015, 22:32:38 UTC | Added a section on error handling | 21 September 2015, 22:32:38 UTC |
| 0e7bb0e | Aaron Petkau | 21 September 2015, 22:14:26 UTC | Updated test data to work at a coverage of 15 | 21 September 2015, 22:14:26 UTC |
| 04a26a6 | Aaron Petkau | 21 September 2015, 20:56:36 UTC | Changed text for searching tool shed | 21 September 2015, 20:56:36 UTC |
| 9e5a7c0 | Aaron Petkau | 21 September 2015, 20:38:38 UTC | Added numbered bullets | 21 September 2015, 20:38:38 UTC |
| 3431c39 | Aaron Petkau | 21 September 2015, 20:34:24 UTC | type and emphasis | 21 September 2015, 20:34:24 UTC |
