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Created with Raphaël 2.2.08Aug432128Jul26251928Jun9732131May241026Apr2514127531Mar2228Feb17151498327Jan2630Nov254318Oct149Sep726Aug25241930Jul29262322330Jun28108432131May3028272524212019181716151412111087654330Apr2721201514131282129Mar252322191811109122Feb1918161154229Jan2821191814remove api_key from RunWorkflowAddTrackToJbrowse class initRemove unused constants. Factorize code from gga_run_wf scripts (add methods get_library_folders_id_dict, add_dataset_from_library). Script gga_run_wf_add_rnaseq: get api_key from config ; use methods set_galaxy_instance and set_history ; move planemo template to templates dir ; create a dedicated dir for planemo jobs yml files ; get workflow file from constants ; update wf.ga with bam track custom configs (v2)test: Use utilities method to get historyfix: Add identifiersfix: Use galaxy_id in jobfilefix: Init hda id in tracks dictstest: Get lib id with new methodfix: get_libraries methodtest: Use hda ids to find trackstest: Upload trackstest: Update workflow to use hda ids, upload the tracks to history, add params to template input fileMerge branch 'dev' into rnaseq-jbrowse-tracksfix picture permissionMerge branch 'fixes' into 'dev'Fix analysis name because used to order analyses on home pageMove analysis program version, sourcename and date for genome and ogs into input org.ymlMove analysis program version, sourcename and date for genome and ogs into input org.ymlUpdate analysis program version and sourcename. Update .ga with uniprot db.Custom analysisprogram for each analysis (in wf.py)Change param project_url to database. Move to description in org.ymlMerge branch 'add_blastp_interpro_wf' into 'dev'adjust wf constantsAdd .ga for 2orgAdd .garemove unused .ga. Add run_wf_blastp_interpro (no blastx)fix get_organism()back to default modeMerge branch 'project_url' into 'dev'add exampleAdd project_url env variable in tripal serviceMerge branch 'v2.3.1' into 'dev'Fix created dir in 777 modetest: Create symlinks for project libtest: Map volume for galaxy servicetest: Try upload without symlink for trackschore: Typotest: With clean_name not modifiedtest: Remove last character escaping (for bam files)Merge branch 'blast_interpro_new' into 'dev'Factorize get_organisms and get_organism into gga_run_wf_phaeo.py. Set coherent with gga_run_phaeo_jb (self.common, remove methods present in gga_run_wf_phaeo, add --no-invoke-wf arg