Tags give the ability to mark specific points in history as being important
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0.4
aee1e657 · ·## [0.4] - 2024-18-12 ### Breaking changes ### Added - Manage bigwig files as input tracks - Optional 'category' key for extra files. Will replace the path ('extra_file_xxx') in the download page - New option `on_job_fail` in `beauris.yml`: if set to `rerun`, will retry previously failed jobs - Add an option called `check_files_exist` that allows loading the file without automatically verifying all paths. - Verify that yaml files use correct extension (.yml) - Add tags for entities and a method `get_tags()`. - Add methods `load_organisms()` that return list of all organisms and `load_organisms_by_tags()` that returns a list of all organisms filtered by tags. - Add a check in check_fasta to verify maximum number of sequences (to detect fragmented assemblies) - Add a config option to disable auto snp generation for bam files in jbrowse - Added support for the use of remote url in yml files for input data - Added support for compressed input data as `.gz` - Added support for checksum verification of input data with sha256 ### Changed - ogs_check: Added an error message for mRNA having some UTR without CDS subfeatures - stricter validation of versions - Send notification even after merge commits (to the closed MR) - Added resiliency for drmaa runner - Should manage entity unicity differently now (all entities must be unique, except CDS that can have the same ID in a specific gene as a discontinous feature) - OGS_check should manage 'exotic entities' -> All non-coding entities will now be written into an optional 'exotic.gff' file. This file will only be used in jbrowse, and not for functional annotation or GNB. - Added a git pull before commiting locked files to avoid an error in some cases ### Fixed - Manage case where the 'Name' key is set but empty in gff files - Set asset folder and its content to 755/644 permissions - Fixed task .state file has duplicate files in it (#128) - Job exit_code not collected when ci job starts after remote job ending (#148) -
0.3
bf8e24be · ·## [0.3] - 2024-04-02 ### Breaking changes - `deploy_perms` service was renamed `deploy_authelia`, need to be updaed in `beauris.yml` in `tasks` section - `interface_setup` local workflow was renamed `deploy_all`, need to be updated in `gitlab-ci.yml` - `# __GOGEPP3000_RULES__` placeholder in authelia conf file was renamed to `# __BEAURIS_RULES__` - In `beauris.yml`, in `data_locker`>`options`>`pattern_derived`, user `{name}` instead of `{task_id}` - In `beauris.yml`, under `deploy`>`servers`>`staging|production`, new `base_url_restricted` and `url_prefix_restricted` are required - *jbrowse_data_dirs* variable is replaced by *extra_ref_data_dirs*, both in beauris.yml and ansible templates. ### Added - ORSON: add descriptions to fasta and gff files (!19, !20, thanks @Kamassau) - Manage mix of private and public data - Add script to cleanup work dir - Expression data handling (finished) - Add links from blast results to genoboo - Add links from JBrowse/Apollo to genoboo - Add support for extra files at organism and assembly level - Improved Elasticsearch integration - Add management of the 'logging-debug' MR label to set logger to debug - Add basic management of VCF files (TBA: testing) - Cleanup old_data_dir if it exists (it shouldn't) when deploying jbrowse/genoboo/ES - Bot-ris will now send validation error to MR - Bot-ris will not send interface url to MR after deploy - Better check for files in yaml (will check container folders to detect mount / permissions issues) - Support xrefs at assembly and annotation level - Support specific access restriction for Apollo at assembly level ### Changed - Refactored docker deployment code - Fixed unwanted replacement of transcript suffix in transcript/CDS outputs of gffread - Fixed tool_version not updated in locked yml when a tool is rerun in a new version - Changed the way we delete files when deploying interfaces. They can now be deleted after updating. For now, active in genoboo only. - Do not generate Genoboo, Elasticsearch or JBrowse datasets when the crresponding services are disabled - Will raise an error in OGS check if any UTR, CDS or exon is not contained by the parent mRNA, unless the --extend-parent option is passed, in which case the mRNA position will be extended to match - Make common_name optional, and make use of it when provided ### Fixed - Fixed 'run_on_touched_orgs', which was detecting changes 'both ways' - Fixed service clause - Fixed purge() methodes for tracks and additional files - Fixed various issues with mixed_perms deployments -
0.2
eee2502a · ·## [0.2] - 2023-11-10 ### Added - Documentation on [https://beauris.readthedocs.io](https://beauris.readthedocs.io/) - Genoboo integration - Make Ansible templates overridable (#49) - Expression data handling (started) - Implement organism pictures - Elasticsearch integration - jbrowse_data_dirs variable in beauris.yml for additional folders to be mounted in the jbrowse container. ### Changed - Fixed Orson execution (!3) - Reworked Apollo permissions update (!1) - Fix interfaces bugs (#51 and #43) - Fix execution of DRMAA tasks - Add support for DNASeq bams - Change bam_to_wig method (faster, uses less memory) - Fixed unusable date in entities metadata