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https://github.com/apetkau/snvphyl-galaxy
08 February 2024, 10:35:49 UTC
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Revision Author Date Message Commit Date
9fb166e Aaron Petkau 18 November 2015, 21:14:53 UTC Merge branch 'feature/ecoli_example' into 'development' Add correct ecoli tree for documentation See merge request !41 18 November 2015, 21:14:53 UTC
c40c867 csieffert 18 November 2015, 21:09:24 UTC Add correct ecoli tree for documentation 18 November 2015, 21:09:24 UTC
19c6990 Aaron Petkau 17 November 2015, 19:53:37 UTC Merge branch 'ci_planemo_tests' into 'development' Ci planemo tests Initial gitlab ci file. Just runs planemo shed_lint to ensure everything looks good. Only fails on errors and not warnings. Plan to have another branch to fix all the warnings. See merge request !40 17 November 2015, 19:53:37 UTC
d786f9d Philip Mabon 17 November 2015, 19:47:47 UTC Merge branch 'fix/release-0.3-tools' into 'development' Fix/release 0.3 tools This fixes some issues that came up after merging release-0.3 into development. In particular, the `./scripts/full_install.sh` needs some install steps added. ALso the snvphyl tool version numbers have been updated to all be `1.6.0-dev`. I figure we can keep this version number as we develop (or keep on incrementing it if necessary) until it's time to release, at which point we can drop the `dev` part. See merge request !39 17 November 2015, 19:47:47 UTC
91c2e83 Aaron Petkau 17 November 2015, 17:44:50 UTC Updating workflow with updates from vcf2pseudoalign 17 November 2015, 17:44:50 UTC
aef3f1a Aaron Petkau 17 November 2015, 15:32:25 UTC Fixed paths of tools 17 November 2015, 15:32:25 UTC
58b91bf Aaron Petkau 17 November 2015, 15:23:47 UTC Updating git commit for dependencies 17 November 2015, 15:23:47 UTC
b9d9ad7 Aaron Petkau 17 November 2015, 15:22:31 UTC Fixed up vcf2pseudoalignment 17 November 2015, 15:22:31 UTC
d2e01be Takadonet 17 November 2015, 14:46:11 UTC changed that we only fail when we get an error and not warning. Might change it later. But for now, want to get the basic test working first 17 November 2015, 14:46:11 UTC
563dcc5 Aaron Petkau 17 November 2015, 14:14:31 UTC Updated to port 9009 17 November 2015, 14:14:31 UTC
3433ce1 Aaron Petkau 17 November 2015, 00:35:45 UTC Updated to 0.5 17 November 2015, 00:35:45 UTC
dd6774b Aaron Petkau 17 November 2015, 00:35:07 UTC Added 0.5 workflow 17 November 2015, 00:35:07 UTC
bef7e25 Aaron Petkau 17 November 2015, 00:11:53 UTC Updating from 1.5 to 1.6-dev 17 November 2015, 00:11:53 UTC
8836620 Aaron Petkau 17 November 2015, 00:00:20 UTC Added additional commands to install package/suite_snvphyl 17 November 2015, 00:00:20 UTC
4b7f0da Aaron Petkau 16 November 2015, 23:25:06 UTC MERGE release-0.3 16 November 2015, 23:25:06 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
0353720 Takadonet 16 November 2015, 17:31:39 UTC changed fail level and using system wide planemo instead of my copy. Hoping fail level of 'warn' will causes the CI test to fail 16 November 2015, 17:31:39 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
b3f37bd Takadonet 13 November 2015, 21:45:26 UTC using my local user planemo to test out shed_lint 13 November 2015, 21:45:26 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
af9ffab Takadonet 13 November 2015, 20:02:45 UTC test 13 November 2015, 20:02:45 UTC
3a857e1 Takadonet 13 November 2015, 19:58:27 UTC initial upload of gitlab file... 13 November 2015, 19:58:27 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
c4048c2 Aaron Petkau 12 November 2015, 21:40:13 UTC Merge branch 'fix_toolshed_install' into 'development' added extra parameter to ensure it will work with future galaxy releases. Still works with 'master' and currently releases branches. Needed a redirect parameter... everytime for some reason. See merge request !36 12 November 2015, 21:40:13 UTC
3686d3c Takadonet 12 November 2015, 19:59:48 UTC changed the redirect to work for any toolshed url. Changed curl command to be easier to run all the POST parameters 12 November 2015, 19:59:48 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
dcfa2ec Takadonet 12 November 2015, 16:34:14 UTC added extra parameter to ensure it will work with future galaxy releases. Still works with 'master' and currentl releases branches 12 November 2015, 16:34:14 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
36a1381 Aaron Petkau 06 November 2015, 21:49:26 UTC Merge branch 'remove_unneeded_perl_dep' into 'development' Remove unneeded perl dep To address issue #43 . Tested on local toolshed and galaxy. Tools run correctly and do not see the error anymore! See merge request !35 06 November 2015, 21:49:26 UTC
640d691 Takadonet 06 November 2015, 21:46:49 UTC forgot again.... to increment version number 06 November 2015, 21:46:49 UTC
4befeb3 Aaron Petkau 06 November 2015, 20:43:56 UTC Merge branch 'multiple_thread_verify_mapping' into 'development' Multiple thread verify mapping Just added the $GALAXY_SLOTS to the xml. It will default to 1 core if environment variable is not present. So works on the command line. Allows galaxy admins to speed up the tool. Address issue #29 See merge request !34 06 November 2015, 20:43:56 UTC
e7b3b6b csieffert 06 November 2015, 20:25:38 UTC Merge remote-tracking branch 'origin/fix/snvphyl-0.2-docs' into development 06 November 2015, 20:25:38 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
bca285a Takadonet 05 November 2015, 20:17:16 UTC increment version numbers again because previous merged branch already did 05 November 2015, 20:17:16 UTC
faf687a Takadonet 05 November 2015, 15:25:18 UTC Merge branch 'development' into remove_unneeded_perl_dep 05 November 2015, 15:25:18 UTC
a5cd258 Takadonet 05 November 2015, 15:21:59 UTC increment tool version 05 November 2015, 15:21:59 UTC
ce48152 Takadonet 05 November 2015, 15:11:33 UTC Merge branch 'development' into multiple_thread_verify_mapping 05 November 2015, 15:11:33 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
4dce3da Aaron Petkau 04 November 2015, 20:06:43 UTC Merge branch 'selecting_strains_vcf2pseudo' into 'development' Add ability to include/exclude strains in vcf2pseudo. Also quick setup scripts for local toolshed Setup scripts are really rough but it gets the jobs done. Only catch is that you have to create an admin user with api key generated AND needs to have public name 'nml'. Otherwise it should be simple as running full_install.sh with api_key and toolshed url. i.e full_install.sh API_KEY http://localhost:9009. Uinsg the script above, tested the new xml for vcf2pseudoalignment and all is working. Did not add any more tests to the xml because waiting till we have it working on the gitlab CI server first. Cheers See merge request !31 04 November 2015, 20:06:43 UTC
a549599 Takadonet 04 November 2015, 18:48:23 UTC silent the html response from curl when creating admin user. added echo statement 04 November 2015, 18:48:23 UTC
44c8001 Takadonet 04 November 2015, 17:48:40 UTC added little more docs 04 November 2015, 17:48:40 UTC
cc38847 Takadonet 04 November 2015, 16:48:07 UTC deleted old one 04 November 2015, 16:48:07 UTC
5d2af3f Takadonet 04 November 2015, 16:47:51 UTC updated the InstallLocalToolShed.md file 04 November 2015, 16:47:51 UTC
ab76bee Takadonet 04 November 2015, 16:03:30 UTC admin only needs to pass full url to toolshed. full_install.sh will output both admin username,password and api key. Added some error checking but more is probably needed 04 November 2015, 16:03:30 UTC
3112986 Aaron Petkau 04 November 2015, 14:34:22 UTC Adding link for ecoli examples which didn't get merged in 04 November 2015, 14:34:22 UTC
94e6093 Takadonet 04 November 2015, 14:29:28 UTC forgot to increment version number 04 November 2015, 14:29:28 UTC
e1efe29 Aaron Petkau 04 November 2015, 14:29:21 UTC Merge branch 'feature/ecoli_example' into 'development' Feature/ecoli example Hi Aaron, This is the draft for the ecoli usage example to include in the documentation. It has a lot of overlap with the listeria example that we already have. Let me know of any changes you would like. Thanks! See merge request !27 04 November 2015, 14:29:21 UTC
9949ec0 Takadonet 30 October 2015, 16:50:11 UTC changed permission to executable... 30 October 2015, 16:50:11 UTC
bac04a9 Takadonet 30 October 2015, 16:46:25 UTC resolved conflicts. Took the newest version of package_snvphyl and removed perl 5.18.1 because not needed 30 October 2015, 16:46:25 UTC
8dee14c Takadonet 30 October 2015, 14:36:17 UTC added the ability to multiple thread based on $GALAXY_SLOTS, if not defined, it will use one core by default 30 October 2015, 14:36:17 UTC
6215a78 Aaron Petkau 29 October 2015, 14:29:57 UTC Updated docker for snvphyl 0.3 29 October 2015, 14:29:57 UTC
9dbd3d6 Takadonet 28 October 2015, 17:00:59 UTC changed to latest commit on development branch. Added the ability to use include/exclude files to vcf2pseudoalignment script 28 October 2015, 17:00:59 UTC
f214f6b Takadonet 28 October 2015, 16:59:48 UTC some quick and dirty scripts to setup a toolshed with all the users,categories,capsules and NML tools in one script! Caution, sitll need to make one admin user by hand with public name 'nml' and API key 28 October 2015, 16:59:48 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
a5832f6 csieffert 20 October 2015, 18:51:10 UTC Small grammar change. 20 October 2015, 18:51:10 UTC
77d9751 csieffert 20 October 2015, 18:47:02 UTC Adding E.coli result download to the page. 20 October 2015, 18:47:02 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
82e3fd2 csieffert 15 October 2015, 20:10:18 UTC Changes requested in merge request 15 October 2015, 20:10:18 UTC
738758f csieffert 15 October 2015, 17:14:29 UTC Added results specific to the ecoli run, altered text to reflect ecoli results and workflow 15 October 2015, 17:14:29 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
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