| 7709779 | dependabot[bot] | 03 September 2024, 22:16:36 UTC | Bump actions/download-artifact from 3 to 4.1.7 in /.github/workflows Bumps [actions/download-artifact](https://github.com/actions/download-artifact) from 3 to 4.1.7. - [Release notes](https://github.com/actions/download-artifact/releases) - [Commits](https://github.com/actions/download-artifact/compare/v3...v4.1.7) --- updated-dependencies: - dependency-name: actions/download-artifact dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> | 03 September 2024, 22:20:05 UTC |
| cca536a | Peter Cock | 26 August 2024, 09:07:06 UTC | black 24.8.0 | 26 August 2024, 09:07:38 UTC |
| 68ce195 | Peter Cock | 17 June 2024, 01:47:48 UTC | Update make_nr to latest Biopythn on BioContainers See https://github.com/BioContainers/containers/tree/master/biopython Hopefully this fixes a recent CI failure about deprecations: [DEPRECATION NOTICE] Docker Image Format v1 and Docker Image manifest version 2, schema 1 support is disabled by default and will be removed in an upcoming release. Suggest the author of quay.io/biocontainers/biopython:1.67--np112py36_0 to upgrade the image to the OCI Format or Docker Image manifest v2, schema 2. More information at https://docs.docker.com/go/deprecated-image-specs/. | 17 June 2024, 01:47:52 UTC |
| 45f1384 | Peter Cock | 22 February 2024, 14:53:50 UTC | Include all_fasta.loc.sample in .shed.yml File was added in #164. | 22 February 2024, 14:53:50 UTC |
| 028e3e8 | elischberg | 22 February 2024, 11:49:59 UTC | Add genomes on server functionality (#164) * Add new new option for nucl database - Genome on server * Adjust Tests * test corrected and further changes by @wm75 * Update tools/ncbi_blast_plus/ncbi_makeblastdb.xml * Update Version-Suffix and README * Add missing README doc meesage for VERSION-SUFFIX 1 Co-authored-by: Wolfgang Maier <maierw@posteo.de> | 22 February 2024, 11:49:59 UTC |
| 2dd12dc | Matthias Bernt | 19 November 2023, 18:33:41 UTC | get_species_taxids: fix sed there seem to be now spaces around `:` also add some quotes | 19 November 2023, 21:30:13 UTC |
| d63652a | Peter Cock | 26 October 2023, 12:14:04 UTC | Update change log | 26 October 2023, 12:14:04 UTC |
| e5ff349 | Peter Cock | 11 September 2023, 17:32:37 UTC | Update tests for NCBI BLAST+ 2.14.1 $ tools/ncbi_blast_plus/update_test_files.sh | 26 October 2023, 10:07:41 UTC |
| eb0de4a | Peter Cock | 22 September 2023, 14:50:00 UTC | Remove TODO comment in tool command template | 26 October 2023, 10:07:41 UTC |
| 1dba6f1 | Peter Cock | 11 September 2023, 16:01:01 UTC | Wrap NCBI BLAST+ 2.14.1 Would close issue #146 | 26 October 2023, 10:07:41 UTC |
| 385cf57 | Peter Cock | 24 October 2023, 10:13:50 UTC | No more Galaxy mailing list | 24 October 2023, 10:15:25 UTC |
| 9e81ae1 | Peter Cock | 18 October 2023, 10:44:50 UTC | Remove reference to TravisCI in README | 18 October 2023, 10:44:50 UTC |
| fff17b3 | Peter Cock | 22 September 2023, 14:30:40 UTC | Follow IUC and hard code flake8 extras This was breaking after #158 was merged | 22 September 2023, 14:30:50 UTC |
| 193a2fb | Peter Cock | 22 September 2023, 14:19:50 UTC | Update GitHub CI as per IUC repository Files copied from https://github.com/galaxyproject/tools-iuc/tree/main/.github/workflows Note we have a different owner name, and more flake8 checks | 22 September 2023, 14:23:51 UTC |
| f4a64e1 | Peter Cock | 16 September 2023, 17:17:25 UTC | Fix stray characters from editor I think a rogue keypress in emacs may have done that... | 16 September 2023, 17:17:25 UTC |
| 06c7db9 | Peter Cock | 20 March 2023, 09:55:49 UTC | Apply black v23.1.0 Note they changed the formatting for power operator | 20 March 2023, 09:56:11 UTC |
| 716fba7 | Peter Cock | 19 December 2022, 09:16:15 UTC | Comment out tests in ncbi_deltablast_wrapper.xml Sadly using ``.tt_skip`` to ignore the file is not working. These tests ought to work, but we'd have to have installed the (large) default domain database on the continuous integration platform, see also #18. | 19 December 2022, 09:16:15 UTC |
| ead637b | Peter Cock | 19 December 2022, 09:14:03 UTC | Can't skip individual tools? This ignore list is not working as desired, specifically we're getting 4 failures from ``ncbi_deltablast_wrapper`` (due to missing domain databases). It is unclear if ``tools/ncbi_blast_plus/ncbi_psiblast_wrapper.xml`` is skipped, it currently has no tests defined. However, ``tools/reciprocal_best_hits/reciprocal_best_hits.xml`` do seem to get skipped (we do see test results from the similarly named ``tools/blast_rbh/blast_rbh.xml``) [ci skip] | 19 December 2022, 09:14:03 UTC |
| fcaef83 | Peter Cock | 06 December 2022, 16:28:12 UTC | Fix typo [ci skip] | 06 December 2022, 16:28:12 UTC |
| 86edfae | Peter Cock | 06 December 2022, 16:27:49 UTC | v0.0.11 also adopted python 3 syntax [ci skip] | 06 December 2022, 16:27:49 UTC |
| 4e9aad9 | Peter Cock | 06 December 2022, 16:01:03 UTC | Clarify comment in blast_rbh_report.py This does not (currently) have a Galaxy wrapper | 06 December 2022, 16:01:03 UTC |
| a6b5567 | Matthias Bernt | 06 December 2022, 14:39:20 UTC | fix slash workflow syntax | 06 December 2022, 14:46:29 UTC |
| 47a3220 | M Bernt | 06 December 2022, 14:29:51 UTC | Run slash command only if PAT is defined (#151) See https://github.com/peter-evans/slash-command-dispatch | 06 December 2022, 14:29:51 UTC |
| 940f223 | Peter Cock | 06 December 2022, 14:19:47 UTC | Restore the tool test skip entries from TravisCI era e.g. We can't test ncbi_deltablast_wrapper.xml without downloading a large protein domain database. | 06 December 2022, 14:24:13 UTC |
| 40bc882 | Peter Cock | 06 December 2022, 14:03:26 UTC | Include the flake8 plugins once used on TravisCI Cross reference https://github.com/galaxyproject/tools-iuc/issues/4988 | 06 December 2022, 14:03:48 UTC |
| 50e4414 | Peter Cock | 06 December 2022, 14:03:03 UTC | Remove trailing whitespace | 06 December 2022, 14:03:03 UTC |
| a7e9150 | Matthias Bernt | 06 December 2022, 13:48:15 UTC | introduce flake8 requirements | 06 December 2022, 14:00:00 UTC |
| 67f522b | Peter Cock | 06 December 2022, 13:35:58 UTC | Version bump for BLAST+ wrappers More important now as will be using automated deployment to test and main tool shed. | 06 December 2022, 13:39:21 UTC |
| 7fda77c | Peter Cock | 06 December 2022, 13:35:30 UTC | Correction: db_opts.db_opts_selector would be db, histdb, or file | 06 December 2022, 13:35:30 UTC |
| 20fe83e | Peter Cock | 06 December 2022, 13:10:37 UTC | Silence deltablast warning about using threads with subject This is to supress this warning on stdout: 'num_threads' is currently ignored when 'subject' is specified. | 06 December 2022, 13:11:16 UTC |
| f740d1b | Peter Cock | 06 December 2022, 13:05:57 UTC | Fix text XML in ncbi_blastp_wrapper.xml Spotted with planemo lint, this (harmless?) glitch had been here a long time. | 06 December 2022, 13:11:16 UTC |
| d4a847e | Peter Cock | 06 December 2022, 12:51:12 UTC | Replace TravisCI etc badge with GitHub Actions badge [ci skip] | 06 December 2022, 12:51:12 UTC |
| 98f8f7c | Peter Cock | 06 December 2022, 12:06:58 UTC | Update TIGRFAMs TFP URL (failed linting) | 06 December 2022, 12:06:58 UTC |
| 09726d7 | M Bernt | 06 December 2022, 11:47:58 UTC | GitHub actions (#149) * add github actions * remove travis stuff * exclude datatypes and workflows * link test data * update skipped tools * switch to correct repo name | 06 December 2022, 11:47:58 UTC |
| 98c583b | Peter Cock | 06 December 2022, 11:33:52 UTC | reorder-python-imports matches flake8-import-order pycharm style (and pep8) It does not match flake8-import-order smarkets due to case sorting. [ci skip] | 06 December 2022, 11:33:52 UTC |
| c8d352c | Peter Cock | 06 December 2022, 11:04:04 UTC | Run reorder-python-imports 3.9.0 [ci skip] | 06 December 2022, 11:11:51 UTC |
| f096f1c | Peter Cock | 18 November 2022, 12:43:41 UTC | Fix typo in script description [ci skip] | 18 November 2022, 12:43:41 UTC |
| 9d2b6da | mthang | 07 June 2022, 10:39:42 UTC | update ncbi_blastn_wrapper.xml - window_size (#144) * Fix duplication of -window_size in command line * update version suffix in ncbi_macro.xml * update README.rst Closes #143. | 07 June 2022, 10:39:42 UTC |
| d4bbed9 | Nate Coraor | 27 May 2022, 14:50:00 UTC | Add explicit Python requirements to tools that appear to require it | 27 May 2022, 18:30:28 UTC |
| 7eaaba2 | M Bernt | 29 March 2022, 14:47:15 UTC | DB quoting and taxid improvements (#136) * properly quote cached databases https://www.ncbi.nlm.nih.gov/books/NBK279669/ * add wrapper for get_species_taxids.xml * allow the input of taxid lists | 29 March 2022, 14:47:15 UTC |
| 1e3b152 | Peter Cock | 18 March 2021, 12:37:58 UTC | Update make_nr change log | 18 March 2021, 12:37:58 UTC |
| c943d89 | Peter Cock | 18 March 2021, 12:37:51 UTC | Update comment [ci skip] | 18 March 2021, 12:37:51 UTC |
| 4a183a8 | M Bernt | 18 March 2021, 12:33:01 UTC | fix make_nr if no dups exist (#137) The branch for the case that no duplicates exist failed because it assumed that the input was a single file | 18 March 2021, 12:33:01 UTC |
| 47e892e | Matthias Bernt | 07 December 2020, 09:22:50 UTC | properly quote chached databases https://www.ncbi.nlm.nih.gov/books/NBK279669/ | 17 March 2021, 16:38:25 UTC |
| f5107b6 | Peter Cock | 17 March 2021, 14:26:26 UTC | Ignore flake8 B902 blind except Exception: statement For now willing to ignore this as testing assorted operating systems for the right exception is hard. | 17 March 2021, 15:14:58 UTC |
| cae95c7 | M Bernt | 29 November 2020, 14:10:33 UTC | make blast dbs non-optional (#135) since multiple="true" selects are optional by default the tools can be submitted without selecting a DB which leads to a tool error. | 29 November 2020, 14:10:33 UTC |
| 1c8f1bd | Peter Cock | 27 November 2020, 16:49:08 UTC | Fix sorting of release notes [ci skip] | 27 November 2020, 16:49:08 UTC |
| 3ac00a9 | peterjc | 09 September 2020, 22:30:19 UTC | Target BLAST+ 2.10.1 | 10 September 2020, 13:16:29 UTC |
| 0ff8cfa | Anthony Bretaudeau | 07 September 2020, 11:58:10 UTC | blastn word size needs >=4 now | 10 September 2020, 13:16:29 UTC |
| a2839f8 | peterjc | 09 September 2020, 22:25:39 UTC | tools/ncbi_blast_plus/update_test_files.sh with BLAST+ 2.10.1 | 10 September 2020, 13:16:29 UTC |
| c667c8d | Peter Cock | 09 September 2020, 21:17:15 UTC | Explicitly build older v4 BLAST DBs In preparation for wrapping NCBI BLAST+ 2.10, which adds support for setting the preferred DB version. Need to wait for new v5 BLAST DB datatypes to be in a released version of Galaxy before using them. See https://github.com/galaxyproject/galaxy/pull/9939 | 10 September 2020, 13:16:29 UTC |
| eb20367 | Peter Cock | 10 September 2020, 10:29:27 UTC | Thank Anthony Bretaudeau | 10 September 2020, 10:29:27 UTC |
| 5fde156 | Peter Cock | 09 September 2020, 17:19:47 UTC | Clarify release notes for blast_rbh | 09 September 2020, 22:11:51 UTC |
| b6b0c5f | Anthony Bretaudeau | 06 July 2020, 13:15:51 UTC | update blast_rbh too | 09 September 2020, 22:11:51 UTC |
| f17fd47 | Peter Cock | 09 September 2020, 17:16:15 UTC | (re)creation of rhodopsin_nucs.no_gi.region.fasta | 09 September 2020, 22:11:50 UTC |
| c207aed | Anthony Bretaudeau | 23 April 2020, 13:24:54 UTC | Update to 2.9.0 Rebased and conflicts resolved by Peter Cock, also updated the deltablast test output (needs large download to run, not done on TravisCI). | 09 September 2020, 22:10:36 UTC |
| c4c000a | peterjc | 09 September 2020, 22:00:53 UTC | Updated paths, now have cdd_delta in $BLASTDB | 09 September 2020, 22:10:33 UTC |
| 3f9f39a | Peter Cock | 09 September 2020, 15:09:55 UTC | Don't deploy packages or datatypes These are obsolete (using bioconda for dependencies, and datatypes are built into Galaxy once again). | 09 September 2020, 15:09:55 UTC |
| 0c82b9e | Peter Cock | 09 September 2020, 12:02:53 UTC | Update README with blastdbcmd work | 09 September 2020, 13:45:45 UTC |
| 958802c | Peter Cock | 08 September 2020, 15:16:25 UTC | Define @DBCMD_OPTS@, fix inconsistent label macro name Changed @ON_DBCMD_SUBJECT@ / @ON_DB_SUBJECT_ORIGIN@ to @ON_DBCMD_OPTS@ | 09 September 2020, 13:45:45 UTC |
| 503c837 | Peter Cock | 08 September 2020, 15:06:06 UTC | Restore else | 09 September 2020, 13:45:45 UTC |
| 446daf8 | Frahiriart | 12 June 2020, 08:53:25 UTC | Support history DB in blastdbcmd wrapper Modification of input of the function input_conditional_choose_db_type (Rebased and conflicts resolved by Peter Cock) | 09 September 2020, 13:45:45 UTC |
| 71a7deb | Peter Cock | 09 September 2020, 11:10:38 UTC | Use multiple DB in blastdbcmd -entry test | 09 September 2020, 12:27:49 UTC |
| d50e108 | Peter Cock | 09 September 2020, 10:24:19 UTC | Test blastdbcmd -info with multiple databases | 09 September 2020, 12:27:49 UTC |
| e8bf3d1 | Peter Cock | 09 September 2020, 11:43:49 UTC | Apply multiple DB fix for blastdbcmd -info too | 09 September 2020, 12:27:49 UTC |
| e867c75 | Peter Cock | 09 September 2020, 10:22:22 UTC | Only check first 3 lines of blastdbcmd -info output This avoids the changeable date and file path, plus the DB v4 verus v5 line added in later releases of NCBI BLAST (would like to include that really but seems a reasonable compromise). | 09 September 2020, 12:27:49 UTC |
| f3980e7 | Peter Cock | 08 September 2020, 15:56:06 UTC | Adopt @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ See https://github.com/galaxy-iuc/standards/pull/59/ | 08 September 2020, 20:12:56 UTC |
| 8b5b3a7 | Peter Cock | 08 September 2020, 15:36:01 UTC | Reverse chronological change log Fixed a few long lines too. | 08 September 2020, 15:39:01 UTC |
| f726ee4 | Peter Cock | 21 August 2020, 10:38:20 UTC | Update main README on packages and datatypes | 21 August 2020, 11:57:22 UTC |
| 897dd39 | Peter Cock | 21 August 2020, 10:11:53 UTC | Clarify Tool Shed datatypes are obsolete | 21 August 2020, 11:57:22 UTC |
| 173362a | Peter Cock | 21 August 2020, 10:07:50 UTC | TravisCI: Stop using our local datatype definitions | 21 August 2020, 11:57:22 UTC |
| bd6708e | Peter Cock | 21 August 2020, 09:36:27 UTC | Use <tool ... profile="16.10"> to get datatypes This was the release of galaxy to have the datatypes for BLAST XML and DB added. This replaces explicit use of the datatypes on the tool shed via the legacy repository_dependencies.xml file. | 21 August 2020, 11:57:22 UTC |
| e83d068 | Peter Cock | 20 August 2020, 14:00:12 UTC | Remove redundant repository_dependencies.xml files Can now assume BLAST datatypes are included with Galaxy | 20 August 2020, 19:29:22 UTC |
| 0df1d11 | Peter Cock | 20 August 2020, 13:49:46 UTC | Remove obsolete tool_dependencies.xml files. Only very very old instances of Galaxy will still use these for dependency resolution. | 20 August 2020, 19:29:22 UTC |
| e31327e | Peter Cock | 20 August 2020, 13:24:45 UTC | TravisCI: Galaxy supports Python 3 now; check black Misc setup simiplications too, see similar work on the pico_galaxy and galaxy_mira repositories. | 20 August 2020, 19:29:22 UTC |
| 0a855ef | peterjc | 21 October 2019, 12:49:00 UTC | Galaxy dev branch can use longer filenames than expected e.g. INFO [galaxy.tool_util.verify] ## files diff on '/tmp/tmphx0IeVtblastn_four_human_vs_rhodopsin.html' and '/tmp/tmpB1EonStblastn_four_human_vs_rhodopsin.html': lines_diff = 8, found diff = 10 ... JobOutputsError: History item different than expected, difference (using diff): ( /tmp/tmphx0IeVtblastn_four_human_vs_rhodopsin.html v. /tmp/tmpB1EonStblastn_four_human_vs_rhodopsin.html ) --- local_file +++ history_data @@ -16,7 +16,10 @@ -Database: User specified sequence set (Input: rhodopsin_nucs.fasta). +Database: User specified sequence set (Input: +/tmp/tmprQgXwd/tmpIAL5Yb/tmpSmGl1Z/database/job_working_directory_G1 +MyfC/000/178/task_0/dataset_7e71a821-e262-4330-aa72- +e7fcaab12a8e.dat). 6 sequences; 10,296 total letters @@ -328,7 +331,10 @@ Effective search space used: 1049670 - Database: User specified sequence set (Input: rhodopsin_nucs.fasta). + Database: User specified sequence set (Input: +/tmp/tmprQgXwd/tmpIAL5Yb/tmpSmGl1Z/database/job_working_directory_G1 +MyfC/000/178/task_0/dataset_7e71a821-e262-4330-aa72- +e7fcaab12a8e.dat). Posted date: Unknown Number of letters in database: 10,296 Number of sequences in database: 6 | 21 October 2019, 12:49:00 UTC |
| dc20c37 | peterjc | 19 July 2019, 09:24:32 UTC | Restore tool_dependencies.xml, version bump to match tools This is obsolete, but useful for any Galaxy instances still not updated to use conda for dependencies. | 19 July 2019, 09:27:12 UTC |
| 28cb38d | Peter Cock | 19 July 2019, 07:39:59 UTC | Dropped legacy tool_dependencies.xml | 19 July 2019, 07:39:59 UTC |
| 8860d0e | Peter Cock | 19 July 2019, 07:39:13 UTC | Drop tool_dependencies.xml (out of date anyway) This is no longer used on modern versions of Galaxy, and was out of sync with the new requirements mechanism via conda anyway | 19 July 2019, 07:39:13 UTC |
| 3095f19 | Frederic Sapet | 07 May 2019, 15:04:13 UTC | blastdbcmd needs a space separated list of databases | 09 May 2019, 09:40:34 UTC |
| 0a172d2 | peterjc | 01 April 2019, 10:19:35 UTC | Call this refactoring blast_rbh v0.2.0 | 01 April 2019, 11:21:44 UTC |
| b4235c5 | peterjc | 01 April 2019, 09:00:18 UTC | Ran code formatting tool black, edited docstrings Should now pass the flake8 style checks. | 01 April 2019, 11:21:44 UTC |
| 497a34b | Madden, Tom | 20 March 2019, 15:45:29 UTC | Add min_identity and min_coverage as optional parameters to best_hits method | 01 April 2019, 11:21:44 UTC |
| b7abe7d | Madden, Tom | 20 March 2019, 13:07:48 UTC | Remove extra spaces, unused imports, and fix typos | 01 April 2019, 11:21:44 UTC |
| b416dc5 | Madden, Tom | 19 March 2019, 17:35:46 UTC | Move best_hits method to own module, add blast_rph_report.py to only run best_hits | 01 April 2019, 11:21:44 UTC |
| 506c985 | Peter Cock | 20 March 2019, 13:26:28 UTC | Notes on style checks | 20 March 2019, 13:26:28 UTC |
| 7e9f01d | Peter Cock | 22 February 2019, 15:52:09 UTC | Code style black badge [ci skip] | 22 February 2019, 15:52:09 UTC |
| 960f470 | peterjc | 22 February 2019, 14:04:39 UTC | Update flake8 setting after black changes Would like to enforce black via flake8-black plugin, but black requires Python 3.6 and still using Python 2.7 for Galaxy on TravisCI. | 22 February 2019, 14:04:39 UTC |
| c9209f7 | peterjc | 22 February 2019, 13:42:27 UTC | Fix flake8 E501 using max-line-length 88 (black default) | 22 February 2019, 14:03:45 UTC |
| 4e52a86 | peterjc | 22 February 2019, 13:58:44 UTC | Ran Python code formatting tool black | 22 February 2019, 13:58:44 UTC |
| 0ecaf9c | peterjc | 22 February 2019, 13:44:49 UTC | Move flake8 settings to config file Now used for TravisCI and if running flake8 locally, e.g. in a git pre-commit hook. | 22 February 2019, 13:56:52 UTC |
| 1e259a9 | peterjc | 22 February 2019, 13:52:41 UTC | Python 3 fix, flake8 F821 undefined name 'basestring' | 22 February 2019, 13:55:36 UTC |
| d8184ac | Nicola Soranzo | 03 January 2019, 11:38:10 UTC | Remove deprecated ``sudo: false`` from .travis.yml See https://blog.travis-ci.com/2018-11-19-required-linux-infrastructure-migration | 04 January 2019, 10:06:59 UTC |
| 194b23f | Peter Cock | 14 November 2018, 10:31:47 UTC | restructuredtext-lint v1.2 supports directories | 14 November 2018, 10:31:47 UTC |
| 2f8508e | peterjc | 13 November 2018, 10:37:26 UTC | Allow 8byte difference Note sure why this varies locally and on TravisCI... | 13 November 2018, 10:37:26 UTC |
| fcaa51f | peterjc | 09 November 2018, 16:03:42 UTC | Seems cd00003_and_cd00008.pin shrunk slightly with v2.7.1 $ echo "cd00003.smp cd00008.smp" | makeprofiledb -in /dev/stdin -out cd00003_and_cd00008 -title "Just 2 PSSM matrices" Deleted existing BLAST database with identical name. $ makeprofiledb -version makeprofiledb: 2.7.1+ Package: blast 2.7.1, build Sep 20 2018 02:20:26 Note I am using BLAST+ v2.7.1 from BioConda. | 09 November 2018, 16:03:59 UTC |
| 59c7562 | peterjc | 09 November 2018, 15:54:52 UTC | Clarify citation instructions in tool help text [ci skip] | 09 November 2018, 15:54:59 UTC |
| be4256b | peterjc | 09 November 2018, 15:37:42 UTC | Tweak README | 09 November 2018, 15:37:42 UTC |
| fa70c87 | peterjc | 09 November 2018, 15:36:41 UTC | Fix RST markup in help text | 09 November 2018, 15:36:41 UTC |
| 915c276 | peterjc | 09 November 2018, 14:25:51 UTC | Remove completed README entry | 09 November 2018, 14:25:51 UTC |
