Commits · master · Zeller Group / GECCO · GitLab

21 Nov, 2021 13 commits
- Update Galaxy tool wrapper to follow the IUC best practices · 510d8e39
  Martin Larralde authored Nov 21, 2021
  
  510d8e39
- Add missing test file to `tests.test_cli` required for Galaxy tests · 1ef50ba0
  Martin Larralde authored Nov 21, 2021
  
  1ef50ba0
- Make the `galaxy.yml` Actions workflow always push the tool repository · d66ab63d
  Martin Larralde authored Nov 21, 2021
  
  d66ab63d
- Release v0.8.5 · 7c510d1d
  Martin Larralde authored Nov 21, 2021
  
  7c510d1d
- Add Galaxy tool badge to `README.md` [ci skip] · 0e262461
  Martin Larralde authored Nov 21, 2021
  
  0e262461
- Update Galaxy tool file to force GECCO to output a `clusters.tsv` file · 93ab7129
  Martin Larralde authored Nov 21, 2021
  
  93ab7129
- Add a flag to force writing `clusters.tsv` file even when no BGCs were found · 35e9d9de
  Martin Larralde authored Nov 21, 2021
  
  35e9d9de
- Fix link to contribution guide in `README.md` [ci skip] · 84e75c83
  Martin Larralde authored Nov 21, 2021
  
  84e75c83
- Fix broken syntax in `README.rst` file for Galaxy Tool Shed [ci skip] · 6c1bbcab
  Martin Larralde authored Nov 21, 2021
  
  6c1bbcab
- Setup deployment to the Tool Shed from GitHub Actions `galaxy.yml` workflow · 8f6be816
  Martin Larralde authored Nov 21, 2021
  
  8f6be816
- Add Actions workflow to test Galaxy tool wrapper and deployment · c54eb9ef
  Martin Larralde authored Nov 21, 2021
  
  c54eb9ef
- Add Galaxy tool configuration, test files, and Toolshed deployment files to `galaxy` · c3e58a61
  Martin Larralde authored Nov 21, 2021
  
  c3e58a61
- Update output files for BGC0001866 in `tests.test_cli` · 73b81129
  Martin Larralde authored Nov 21, 2021
  
  73b81129
13 Oct, 2021 1 commit
- Make sure to use all detected genes in `gecco annotate` · 707084f1
  Martin Larralde authored Oct 14, 2021
  
  707084f1
25 Sep, 2021 5 commits
- Replace notice of `multiprocessing.cpu_count` in `README.md` [ci skip] · 177b34a6
  Martin Larralde authored Sep 26, 2021
  
  177b34a6
- Release v0.8.4 · bae29fdc
  Martin Larralde authored Sep 26, 2021
  
  bae29fdc
- Bump minimum required `pyrodigal` version to `v0.6.2` · b6a01730
  Martin Larralde authored Sep 26, 2021
  
  b6a01730
- Add basic unit tests for the `gecco convert` subcommand · 50e9d758
  Martin Larralde authored Sep 26, 2021
  
  50e9d758
- Fix various bugs with `gecco convert gbk --format=bigslice` · b044999b
  Martin Larralde authored Sep 26, 2021
  
  b044999b
03 Sep, 2021 1 commit
- Add script block to `layout.html` docs template to track usage of gecco.embl.de · e2fb1515
  Martin Larralde authored Sep 03, 2021
  
  e2fb1515
23 Aug, 2021 6 commits
- Release v0.8.3-post1 · 774d734a
  Martin Larralde authored Aug 23, 2021
  
  774d734a
- Fix wrong default value for `--threshold` being shown in `gecco run` help message · 8050f757
  Martin Larralde authored Aug 23, 2021
  
  8050f757
- Release v0.8.3 · 21960903
  Martin Larralde authored Aug 23, 2021
  
  21960903
- Change default probability threshold for segmentation from 0.4 to 0.3 · 992f682f
  Martin Larralde authored Aug 23, 2021
  
  992f682f
- Mark release `v0.9.0` as yanked in `CHANGELOG.md` · 4303538d
  Martin Larralde authored Aug 19, 2021
  
  4303538d
- Revert back to model from v0.8.2 · 8554595e
  Martin Larralde authored Aug 19, 2021
```
This reverts commit 23c77f2b.
```
  8554595e
10 Aug, 2021 1 commit
- Update internal model to CRF trained with `--select=0.35` and `--p-filter=1e-5` · 23c77f2b
  Martin Larralde authored Aug 10, 2021
  
  23c77f2b
31 Jul, 2021 6 commits
- Release v0.8.2 · f0074786
  Martin Larralde authored Jul 31, 2021
  
  f0074786
- Skip OSX tests when running on a tagged commit to avoid issues downloading Pfam · c693ad89
  Martin Larralde authored Jul 31, 2021
  
  c693ad89
- Update internal InterPro metadata file · 349a7b20
  Martin Larralde authored Jul 31, 2021
  
  349a7b20
- Add the p-value of each domain to the exported `SeqFeature` qualifiers · 6ec0a875
  Martin Larralde authored Jul 31, 2021
  
  6ec0a875
- Avoid counting number of profiles when annotating with an external HMM · 6b9fa43d
  Martin Larralde authored Jul 31, 2021
  
  6b9fa43d
- Fix `gecco run` command requiring code from the Python 3.7 stdlib · c8c6484b
  Martin Larralde authored Jul 31, 2021
  
  c8c6484b
29 Jul, 2021 6 commits
- Release v0.8.1 · 3a94a5d7
  Martin Larralde authored Jul 29, 2021
  
  3a94a5d7
- Filter domains in `gecco run` even without `--model` flag in case a custom HMM is used · 0e75d14e
  Martin Larralde authored Jul 29, 2021
  
  0e75d14e
- Update `gecco run` command to use the `--model` features if a custom model is given · c7a790af
  Martin Larralde authored Jul 29, 2021
  
  c7a790af
- Add tests for the `PyHMMER` whitelist argument · 50a65cc6
  Martin Larralde authored Jul 29, 2021
  
  50a65cc6
- Add missing documentation for `strand` attribute of `gecco.model.Gene` · e3ebda91
  Martin Larralde authored Jul 29, 2021
  
  e3ebda91
- Add an argument to only annotate with certain HMMs in `gecco.hmmer.PyHMMER` · 0f6eff53
  Martin Larralde authored Jul 29, 2021
  
  0f6eff53
28 Jul, 2021 1 commit
- Fix wrong Pfam version in `gecco/hmmer/Pfam.ini` · 1a7670a2
  Martin Larralde authored Jul 28, 2021
  
  1a7670a2