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  • add-logging
  • add-phenotype-to-consensus-tree
  • add-progress-bars
  • add-scoring-matrices-to-resources
  • add_RG_option
  • add_gfa_build_pangenome
  • add_gfa_export
  • add_loading_bars
  • add_panva_queries
  • add_promoter_sequence_analysis
  • add_wgs_roi
  • automatic_skip_core_phylogeny_fix
  • develop protected
  • docker
  • eggnog_fix
  • fasta-validation
  • feature/fix-msa-with-threshold
  • feature/update-msa-with-aa-presence-threshold
  • fix-core-phylogeny-mode
  • fix-indexing-error-add_annotations
  • v4.3.3
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  • v4.3.1
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Created with Raphaël 2.2.014Jul11109843216Jun543216May15141230Apr292825242322181716151411109831Mar282725241413121110328Feb212019181710754321Jan1716159876320Dec1918171613963218Nov14124129Oct28252321161511109827Sep2625241310916Aug1513129876526Jul2518171611227Jun26252421201918171211730May292315129632130Apr29262423191817161598525Mar2220191815Merge branch 'update_dependencies_pantools' into fix_genomelayer_large_pangenomesfix_genomelayer…fix_genomelayer_large_pangenomesMerge branch 'update_to_java21' into 'update_dependencies_pantools'update_dependen…update_dependencies_pantoolsincrement transaction size to 10mupdate changelogfix_blast_for_p…fix_blast_for_panproteomesremove the use of pangenome specific variables when using panproteome for blastimplement a way to commit transaction in betwee dbg construction and another implementation of it for relationshipsMerge branch 'update_precommit_commands' into 'develop'developdevelopMerge branch 'update_dependencies_pantools' into update_to_java21address code review: remove redundant commentsprint lines to be executed for end-to-end test to enable faster debugging in futuretry initializing conda/mamba directlydon't be so strictadd more loggingtry debugging ci/cdspecify home preciselysource the bashrc just in casealso fix conda installation for end-to-end testhopefully fix the path of mamba and conda with the new docker base imagemake pangenome construction exceptions more explicittry another base imagetry another base imageupdate to java 21update git commit plugin and remove some more deprecated methodsupdating dependencies of pantoolsremove all instances of reused transactions, which causes problems in neo4j v5remove node identifiers from cleaning in end-to-end test more consistentlyremove very last instances of use of deprecated IDs of neo4j nodesremove node ID from msa info output files for testing equalitymake sure println is put on the correct lineMerge branch 'develop' into update_dependencies_pantoolsMerge branch 'update_cicd_reference_commit' into 'develop'update reference commit after !274Merge branch 'fix_msa_sequence_information_panproteome' into 'develop'ensure consistent order of sequences for hmGroup MSAupdate changelogfix the columns in sequences.info for panproteome msafix some minor issues that showed up when starting end-to-end testingremoved deprecated use of getId for GO nodesforgot to remove commitputting creation of mrna node map in same transaction to prevent neo4j complaining