| 88b5a52 | John Chilton | 22 June 2017, 21:14:41 UTC | Version 17.9.2 | 22 June 2017, 21:14:41 UTC |
| 5fe6c78 | John Chilton | 22 June 2017, 21:14:32 UTC | Prep next release. | 22 June 2017, 21:14:32 UTC |
| 864a8af | Björn Grüning | 18 June 2017, 18:51:32 UTC | Merge pull request #68 from jmchilton/dev_update Update against the latest galaxy dev branch. | 18 June 2017, 18:51:32 UTC |
| 9eea97d | John Chilton | 17 June 2017, 23:15:53 UTC | Starting work on 17.9.2 | 17 June 2017, 23:15:53 UTC |
| 9f0f4a8 | John Chilton | 17 June 2017, 23:13:41 UTC | Version 17.9.1 | 17 June 2017, 23:13:41 UTC |
| c064350 | John Chilton | 17 June 2017, 23:08:49 UTC | Update against the latest galaxy dev branch. Mostly brings in changes required for mulled-on-demand Singularity. | 17 June 2017, 23:13:20 UTC |
| 9f802a4 | John Chilton | 17 June 2017, 23:12:32 UTC | Prep next release. | 17 June 2017, 23:12:32 UTC |
| 7b878ce | John Chilton | 17 June 2017, 23:02:12 UTC | Merge pull request #67 from galaxyproject/container_size increase container size by default | 17 June 2017, 23:02:12 UTC |
| 66ebfa4 | Björn Grüning | 17 June 2017, 13:38:58 UTC | Need some sleep | 17 June 2017, 13:38:58 UTC |
| e4fd624 | Björn Grüning | 17 June 2017, 13:30:43 UTC | /data/dist/ | 17 June 2017, 13:30:43 UTC |
| b9edf28 | Björn Grüning | 17 June 2017, 12:41:15 UTC | quoting fixes | 17 June 2017, 12:41:15 UTC |
| fc99a08 | Björn Grüning | 17 June 2017, 12:36:40 UTC | this was not expected | 17 June 2017, 12:36:40 UTC |
| 85d5f2a | Björn Grüning | 17 June 2017, 12:02:56 UTC | improve container size selection | 17 June 2017, 12:02:56 UTC |
| 97bd9fe | Björn Grüning | 12 June 2017, 20:17:57 UTC | Merge pull request #66 from jmchilton/configure_singularity_dir Allow configuration of Singularity image directory. | 12 June 2017, 20:17:57 UTC |
| a05c1c4 | John Chilton | 12 June 2017, 19:59:24 UTC | Allow configuration of Singularity image directory. This will assist in building Singularity containers on demand for Galaxy (https://github.com/galaxyproject/galaxy/issues/4182). | 12 June 2017, 19:59:24 UTC |
| 9aee908 | John Chilton | 12 June 2017, 02:54:44 UTC | Starting work on 17.9.1 | 12 June 2017, 02:54:44 UTC |
| 09a8bd6 | John Chilton | 12 June 2017, 02:54:11 UTC | Version 17.9.0 | 12 June 2017, 02:54:11 UTC |
| 53f961a | John Chilton | 12 June 2017, 02:33:18 UTC | Prep next release. | 12 June 2017, 02:53:58 UTC |
| a37a224 | John Chilton | 09 June 2017, 18:31:25 UTC | Merge pull request #65 from galaxyproject/hack_for_single Hack to fix generation of single target mulled containers. | 09 June 2017, 18:31:25 UTC |
| 076000e | John Chilton | 09 June 2017, 18:10:50 UTC | Fix small syntax error introduced into invfile.lua for singularity stuff. | 09 June 2017, 18:10:50 UTC |
| 3b8062d | John Chilton | 09 June 2017, 17:56:30 UTC | Hack to fix generation of single target mulled containers. | 09 June 2017, 17:56:30 UTC |
| 269e515 | John Chilton | 09 June 2017, 14:17:38 UTC | Merge pull request #64 from galaxyproject/singularity add support for generating singularitiy containers | 09 June 2017, 14:17:38 UTC |
| 08538c8 | Björn Grüning | 09 June 2017, 07:31:13 UTC | pep8 | 09 June 2017, 07:31:13 UTC |
| 62de3b1 | Björn Grüning | 09 June 2017, 07:27:55 UTC | remove unused docker conf | 09 June 2017, 07:27:55 UTC |
| 0fdeeed | Bjoern Gruening | 09 June 2017, 07:25:04 UTC | Merge branch 'singularity' of https://github.com/galaxyproject/galaxy-lib into singularity | 09 June 2017, 07:25:04 UTC |
| 0d66744 | Bjoern Gruening | 09 June 2017, 07:24:13 UTC | change singularity image permissions | 09 June 2017, 07:24:13 UTC |
| 76d73b9 | Björn Grüning | 08 June 2017, 21:55:04 UTC | Merge branch 'master' into singularity | 08 June 2017, 21:55:04 UTC |
| f659ee4 | Björn Grüning | 08 June 2017, 21:43:00 UTC | Merge pull request #63 from galaxyproject/mulled_containers_v2 Implement mulled containers v2. | 08 June 2017, 21:43:00 UTC |
| 20de8ae | Bjoern Gruening | 08 June 2017, 19:39:36 UTC | add support for generating singularitiy containers | 08 June 2017, 20:15:44 UTC |
| 51b5900 | John Chilton | 08 June 2017, 18:49:33 UTC | Switch default mulled namespace to biocontainers (from mulled). | 08 June 2017, 19:27:51 UTC |
| c81ff8a | John Chilton | 08 June 2017, 02:29:43 UTC | Implement mulled containers v2. For a given set of packages and versions, the v1 containers had names and versions like: mulled-v1-<hash_of_packages_and_versions>:<build_number> Here the quay.io repository has a unique name per combination of packages and versions - and the repository tag (the part after the :) is solely used to specify a build number (a mechanism allowing us to increment and rebuild containers with same recipes if they are broken in some way - mirroring closely the conda build number). The version of the hash looks like: mulled-v2-<hash_of_packages>:<hash_of_versions>-<build_number> Here a repository is only created for each combination of packages - different combinations of versions are represented as different tags within that repository. This commit breaks backward compatibility (of a feature configured with a beta label) - but since we are aware of no biocontainers published in the wild it would probably be a okay idea to eliminate the backward compatability. | 08 June 2017, 19:27:51 UTC |
| 50bfea7 | John Chilton | 06 June 2017, 16:42:48 UTC | Merge pull request #62 from jmchilton/updated_against_latest_dev Update against the latest Galaxy dev branch. | 06 June 2017, 16:42:48 UTC |
| f2bed38 | John Chilton | 06 June 2017, 16:33:14 UTC | Fixup util/postfork changes from Galaxy dev. | 06 June 2017, 16:33:14 UTC |
| 76ba57a | John Chilton | 06 June 2017, 14:30:22 UTC | Update against the latest Galaxy dev branch. | 06 June 2017, 16:05:50 UTC |
| 08aaefb | John Chilton | 31 May 2017, 11:13:09 UTC | Starting work on 17.5.12 | 31 May 2017, 11:13:09 UTC |
| a1fcabb | John Chilton | 31 May 2017, 11:12:43 UTC | Version 17.5.11 | 31 May 2017, 11:12:43 UTC |
| fc0419e | John Chilton | 31 May 2017, 11:11:04 UTC | Rev next release. | 31 May 2017, 11:12:37 UTC |
| d529ca2 | John Chilton | 31 May 2017, 11:10:19 UTC | Fix bug in new offline Conda search function. | 31 May 2017, 11:10:19 UTC |
| 3b731a4 | John Chilton | 30 May 2017, 18:41:23 UTC | Fix RST of HISTORY.rst. | 30 May 2017, 18:41:23 UTC |
| 3b02f90 | John Chilton | 30 May 2017, 18:40:03 UTC | Starting work on 17.5.11 | 30 May 2017, 18:40:03 UTC |
| 7f5eea7 | John Chilton | 30 May 2017, 18:39:13 UTC | Version 17.5.10 | 30 May 2017, 18:39:13 UTC |
| d611d4f | John Chilton | 30 May 2017, 18:38:59 UTC | Prep next release. | 30 May 2017, 18:38:59 UTC |
| 45fa0bc | Björn Grüning | 28 May 2017, 18:09:16 UTC | Merge pull request #61 from johanneskoester/master Always cleanup build directory (also in case of errors). | 28 May 2017, 18:09:16 UTC |
| 310dd39 | Johannes Köster | 27 May 2017, 09:40:38 UTC | Always cleanup build directory (also in case of errors). Also do this if the directory is not empty. Question is whether this will always work, because the directory might contain files owned by root? | 27 May 2017, 09:44:47 UTC |
| a97860d | Björn Grüning | 23 May 2017, 00:42:19 UTC | Merge pull request #60 from jmchilton/offline_search Expose offline Conda search option in conda_util.py. | 23 May 2017, 00:42:19 UTC |
| 720e881 | John Chilton | 22 May 2017, 17:48:54 UTC | Expose offline Conda search option in conda_util.py. Probably best to do this is repeatedly doing many searches. | 22 May 2017, 17:49:26 UTC |
| c020939 | John Chilton | 19 May 2017, 20:34:24 UTC | Merge pull request #59 from jmchilton/push_repositories_public More mulled-build-files fixes. | 19 May 2017, 20:34:24 UTC |
| 74abe8a | John Chilton | 19 May 2017, 14:14:11 UTC | Address @bgruening comments on mulled-build-files enhancements. xref https://github.com/galaxyproject/galaxy-lib/pull/59 - Start tags at "0" instead of "1" to match with Conda. - Make stronger assertion about input image names. | 19 May 2017, 14:14:11 UTC |
| 21b4bc5 | John Chilton | 18 May 2017, 18:18:30 UTC | Strip tag from repository creation and checking existing repository. | 18 May 2017, 18:37:08 UTC |
| 70314e3 | John Chilton | 18 May 2017, 18:18:04 UTC | Fixup condition for explicit name. | 18 May 2017, 18:18:04 UTC |
| ba1ae3e | John Chilton | 18 May 2017, 17:40:33 UTC | When using mulled-build-files - specify and explicit image build if unset. This way even the first version has a tag and these can be sorted. | 18 May 2017, 17:42:35 UTC |
| 10b1cf3 | John Chilton | 18 May 2017, 16:37:26 UTC | Properly split on tabs instead of spaces in mulled-build-files. | 18 May 2017, 16:42:09 UTC |
| faf5289 | John Chilton | 18 May 2017, 16:35:35 UTC | Rework rebuilding existing images... - Add --check-published flag for mulled-build*. - Move --force-rebuild to mulled-build-channel - since it was only used there. - Fix bug in rebuild logic previously added. | 18 May 2017, 16:36:33 UTC |
| c3caa4f | John Chilton | 18 May 2017, 16:18:09 UTC | Fix image_build and name_override in mulled_build_files. | 18 May 2017, 16:18:09 UTC |
| c5e7778 | John Chilton | 18 May 2017, 15:57:42 UTC | Fix first use of mulled-build-* for auto-install of Involucro. | 18 May 2017, 15:57:42 UTC |
| 8713ea9 | Björn Grüning | 17 May 2017, 18:51:05 UTC | Merge pull request #58 from jmchilton/push_repositories_public mulled-build-files improvements/fixes. | 17 May 2017, 18:51:05 UTC |
| c192e27 | John Chilton | 16 May 2017, 19:48:32 UTC | mulled-build-files improvements/fixes. - Do not attempt to rebuild already published containers. - Attempt to push repositories as public if supplied an oauth token. | 16 May 2017, 19:50:58 UTC |
| 779b167 | John Chilton | 16 May 2017, 13:33:58 UTC | Starting work on 17.5.10 | 16 May 2017, 13:33:58 UTC |
| c1f6460 | John Chilton | 16 May 2017, 13:33:30 UTC | Version 17.5.9 | 16 May 2017, 13:33:30 UTC |
| 8c0ed48 | John Chilton | 16 May 2017, 13:33:14 UTC | Update HISTORY.rst for new version. | 16 May 2017, 13:33:14 UTC |
| cb25197 | John Chilton | 10 May 2017, 12:58:05 UTC | Merge pull request #56 from galaxyproject/var_image_name add ability to provide a new base image | 10 May 2017, 12:58:05 UTC |
| e5aabd4 | Björn Grüning | 10 May 2017, 07:22:08 UTC | Merge pull request #57 from tom-tan/biocontainers Make mulled-search to search biocontainers instead of mulled repository by default | 10 May 2017, 07:22:08 UTC |
| 2e0346b | Tomoya Tanjo | 10 May 2017, 06:20:02 UTC | Make mulled-search to search biocontainers instead of mulled repository | 10 May 2017, 06:20:02 UTC |
| 7e3a6fe | Bjoern Gruening | 09 May 2017, 21:01:52 UTC | add ability to provide a new base image | 09 May 2017, 21:01:52 UTC |
| 9e88fad | John Chilton | 24 April 2017, 00:30:47 UTC | Starting work on 17.5.9 | 24 April 2017, 00:30:47 UTC |
| 3f67e55 | John Chilton | 24 April 2017, 00:30:05 UTC | Version 17.5.8 | 24 April 2017, 00:30:05 UTC |
| 86fa8c7 | John Chilton | 24 April 2017, 00:29:56 UTC | Prep next release. | 24 April 2017, 00:29:56 UTC |
| 8e8192e | John Chilton | 24 April 2017, 00:27:34 UTC | Merge pull request #55 from galaxyproject/cleanup_after_build Cleanup after build | 24 April 2017, 00:27:34 UTC |
| f05e16e | Björn Grüning | 22 April 2017, 19:33:14 UTC | cleanups | 22 April 2017, 19:33:14 UTC |
| 1ee76ba | Björn Grüning | 22 April 2017, 19:30:09 UTC | poor mans cleanup | 22 April 2017, 19:30:09 UTC |
| c04d722 | John Chilton | 15 March 2017, 13:55:01 UTC | Starting work on 17.5.8 | 15 March 2017, 13:55:01 UTC |
| 22af2f7 | John Chilton | 15 March 2017, 13:54:30 UTC | Version 17.5.7 | 15 March 2017, 13:54:30 UTC |
| a3aab72 | John Chilton | 15 March 2017, 12:20:30 UTC | Prep release notes for a new release. | 15 March 2017, 12:20:30 UTC |
| 218e280 | John Chilton | 14 March 2017, 19:17:51 UTC | Merge pull request #54 from jmchilton/eliminate_default_tool_location_fetcher Eliminate DEFAULT_TOOL_LOCATION_FETCHER since it causes import cycles… | 14 March 2017, 19:17:51 UTC |
| 380f219 | John Chilton | 14 March 2017, 19:14:08 UTC | Eliminate DEFAULT_TOOL_LOCATION_FETCHER since it causes import cycles in Galaxy proper. | 14 March 2017, 19:14:08 UTC |
| 62cdeb0 | John Chilton | 13 March 2017, 03:48:55 UTC | Need to sync this directory also now. | 13 March 2017, 03:48:55 UTC |
| 3b28968 | John Chilton | 13 March 2017, 02:20:38 UTC | Add new fetcher script from #52 to list of modules sync'ed with Galaxy. | 13 March 2017, 02:20:38 UTC |
| caca9a8 | John Chilton | 11 March 2017, 15:42:07 UTC | Update default dependency resolver order... Brings in changes from galaxyproject/galaxy#3708. | 11 March 2017, 17:57:30 UTC |
| a409af0 | John Chilton | 11 March 2017, 15:39:51 UTC | Merge pull request #53 from jmchilton/cwl_update Update CWL modules for upstream work in common-workflow-language/galaxy. | 11 March 2017, 15:39:51 UTC |
| 2fff78c | John Chilton | 11 March 2017, 15:33:48 UTC | Update CWL modules for upstream work in common-workflow-language/galaxy. | 11 March 2017, 15:35:34 UTC |
| 6d53fc7 | John Chilton | 10 March 2017, 20:17:14 UTC | Simplify CondaContext.use_local property. Per recommendation of @nsoranzo. | 10 March 2017, 20:17:14 UTC |
| e3c89e1 | John Chilton | 10 March 2017, 18:23:04 UTC | Merge pull request #52 from jmchilton/location_resolution Add location fetching for Galaxy tools. | 10 March 2017, 18:23:04 UTC |
| b9628eb | John Chilton | 09 March 2017, 20:59:24 UTC | Add location fetching for Galaxy tools. This allows Planemo to do some cool stuff like running CWL tools right from dockstore: planemo run dockstore://quay.io/briandoconnor/dockstore-tool-md5sum job.json But would also be useful for linting tools and such from URLs. | 10 March 2017, 01:19:13 UTC |
| 0bd3065 | John Chilton | 09 March 2017, 13:57:46 UTC | Merge pull request #51 from jmchilton/galaxy_updates_20170309 Bring in Galaxy updates. | 09 March 2017, 13:57:46 UTC |
| 92401b0 | John Chilton | 09 March 2017, 13:46:52 UTC | Bring in Galaxy updates. | 09 March 2017, 13:46:52 UTC |
| 245dafc | John Chilton | 02 March 2017, 00:57:28 UTC | Starting work on 17.5.7 | 02 March 2017, 00:57:28 UTC |
| 15cfaa8 | John Chilton | 02 March 2017, 00:56:55 UTC | Version 17.5.6 | 02 March 2017, 00:56:55 UTC |
| 5a78af8 | John Chilton | 01 March 2017, 13:44:37 UTC | Follow up fixes and HISTORY item for #50. | 01 March 2017, 14:29:07 UTC |
| 82a45e3 | Björn Grüning | 28 February 2017, 18:20:43 UTC | Merge pull request #50 from jmchilton/mulled_options Add more flexibility to mulled operations. | 28 February 2017, 18:20:43 UTC |
| fbaf920 | John Chilton | 28 February 2017, 17:42:29 UTC | Add more flexibility to mulled operations. Clean up verbose handling, make images configurable, and such. The major fix is the addition of allowing a specified version of Conda to be installed before building images - this is required to work around certain packages such ncurses not working under osxfs and conda=4.2. This is fixed with Conda 4.3. Likely this bug is related to https://github.com/conda/conda/issues/3494. | 28 February 2017, 18:04:16 UTC |
| d7bf30f | John Chilton | 27 February 2017, 04:08:16 UTC | Starting work on 17.5.6 | 27 February 2017, 04:08:16 UTC |
| b218249 | John Chilton | 27 February 2017, 04:02:19 UTC | Version 17.5.5 | 27 February 2017, 04:02:19 UTC |
| f7ee808 | John Chilton | 27 February 2017, 04:02:08 UTC | Prep 17.5.5. | 27 February 2017, 04:02:08 UTC |
| 1b7bca6 | John Chilton | 27 February 2017, 03:52:08 UTC | Don't try to --use-local to install conda-build - it doesn't work. | 27 February 2017, 03:52:08 UTC |
| 7aed0da | John Chilton | 27 February 2017, 03:03:10 UTC | Starting work on 17.5.5 | 27 February 2017, 03:03:10 UTC |
| 2c0c04a | John Chilton | 27 February 2017, 03:02:37 UTC | Version 17.5.4 | 27 February 2017, 03:02:37 UTC |
| e78124e | John Chilton | 27 February 2017, 03:02:16 UTC | Prep release of 17.5.4. | 27 February 2017, 03:02:16 UTC |
| 36b2e65 | John Chilton | 27 February 2017, 02:58:17 UTC | Touch up problem with bdacc4d98245411786533bd5c37d5dfa74340e1b. | 27 February 2017, 02:58:17 UTC |
| 3c28e93 | John Chilton | 24 February 2017, 18:27:11 UTC | Update default miniconda install path. Planemo is currently installing miniconda3 to $HOME/miniconda2. | 24 February 2017, 18:29:47 UTC |
| bdacc4d | John Chilton | 24 February 2017, 17:46:00 UTC | If initializing Conda with local packages enabled, ensure conda-build is installed. This is required by Conda. Also provide a flag to force this behavior, when using planemo conda-build should always be installed I think - it is a developer tool after all. | 24 February 2017, 18:29:47 UTC |
