{"push_id":789290245,"size":137,"distinct_size":1,"ref":"refs/heads/master","head":"9a7a0b0a641fb4f0a9a6dea291a6e690650e13e6","before":"b0e1614ffd38fa22f5755b4dbfc4d16b8c3cce37","commits":[{"sha":"5055c252af6174828190374f503d3ae3105be950","author":{"email":"aa5ef0a84f95a8b352d9bda81a0c8ef099dcb88a@ebi.ac.uk","name":"fergalmartin"},"message":"Created new module HiveDownloadNCBIFtpFiles.pm\nThis module represents the first two steps in the assembly loading pipeline. It downloads the structure of the NCBI ftp site for a species and gets the appropriate files. 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It runs the load seq_region script underneath. Basically concats the scaffold and chromo agp files into single files for each coord system and then load contig (from the fasta file), scaffold agp and chromo agp (if present)","distinct":false,"url":"https://api.github.com/repos/Ensembl/ensembl-analysis/commits/e476dfb63d8f36dc8b9e3272d388911b6ca841f8"},{"sha":"45e93e2b5c3fe0e7e52ed794389e78fe90657b56","author":{"email":"aa5ef0a84f95a8b352d9bda81a0c8ef099dcb88a@ebi.ac.uk","name":"fergalmartin"},"message":"Created HiveLoadAssembly.pm\nThis is a hive version of step 6 in the load_assembly script. It takes the mappings in the agp files and loads them into a core db. It does some checking of the information in the files against what is loaded into the db to ensure everything is consistent","distinct":false,"url":"https://api.github.com/repos/Ensembl/ensembl-analysis/commits/45e93e2b5c3fe0e7e52ed794389e78fe90657b56"},{"sha":"ad4a435d1616115824fff2eb83fc278ad888a5aa","author":{"email":"aa5ef0a84f95a8b352d9bda81a0c8ef099dcb88a@ebi.ac.uk","name":"fergalmartin"},"message":"Change to HiveDownloadContigs.pm\nChange the regex to pull out the accession. For some reason I thought the original script was unversioning the accessions and did the same in the code. However this did not make sense, so it now takes out the version too","distinct":false,"url":"https://api.github.com/repos/Ensembl/ensembl-analysis/commits/ad4a435d1616115824fff2eb83fc278ad888a5aa"},{"sha":"b38a52917445953256fe6afa46ad884ff18c5de4","author":{"email":"aa5ef0a84f95a8b352d9bda81a0c8ef099dcb88a@ebi.ac.uk","name":"fergalmartin"},"message":"Change to HiveLoadSeqRegions.pm\nAdded in some code at the start to ensure all parameters have been passed in","distinct":false,"url":"https://api.github.com/repos/Ensembl/ensembl-analysis/commits/b38a52917445953256fe6afa46ad884ff18c5de4"},{"sha":"046b63352af052c8e2a58d9b865bc6c2232b1fb9","author":{"email":"aa5ef0a84f95a8b352d9bda81a0c8ef099dcb88a@ebi.ac.uk","name":"fergalmartin"},"message":"Chage to HiveCreateDatabase.pm\nAdded some flags and code to specify that the populate_production_tables script should be run on the target db","distinct":false,"url":"https://api.github.com/repos/Ensembl/ensembl-analysis/commits/046b63352af052c8e2a58d9b865bc6c2232b1fb9"},{"sha":"f83ca0eb6844f1bc57b746c98fdb1fce408f0b00","author":{"email":"aa5ef0a84f95a8b352d9bda81a0c8ef099dcb88a@ebi.ac.uk","name":"fergalmartin"},"message":"Created HiveSetAndCheckToplevel.pm\nThis is a module to emulate steps 7 and 8 of the load_assembly script. These steps involve setting the toplevel attribute for the toplevel seq regions and then doing various comparisons between what has been loaded into the db (which is dumped out to toplevel.fa) versus what was in the original files that were downloaded","distinct":false,"url":"https://api.github.com/repos/Ensembl/ensembl-analysis/commits/f83ca0eb6844f1bc57b746c98fdb1fce408f0b00"},{"sha":"b693e4ab70dd2a5963ba06d35c1c59c07b09d5f6","author":{"email":"aa5ef0a84f95a8b352d9bda81a0c8ef099dcb88a@ebi.ac.uk","name":"fergalmartin"},"message":"Created HiveSetMetaAndSeqRegionSynonym.pm\nThis module runs step 9 of the load_assembly script. It inserts several values into the meta table and then tries to load seq region synonyms based on the local acc files. It updates the seq_region table to give the chromosomes their humerical names (well with X/Y as well) instead of the accessions. Before doing any of it, it backs up the seq_region and meta tables. The seq_region_synonym table is not backed up because it should be empty at this point anyway","distinct":false,"url":"https://api.github.com/repos/Ensembl/ensembl-analysis/commits/b693e4ab70dd2a5963ba06d35c1c59c07b09d5f6"},{"sha":"cb60775b7569ff4485783c727816bd72bafae222","author":{"email":"aa5ef0a84f95a8b352d9bda81a0c8ef099dcb88a@ebi.ac.uk","name":"fergalmartin"},"message":"Change to HiveSetAndCheckToplevel.pm\nDeleted some comments","distinct":false,"url":"https://api.github.com/repos/Ensembl/ensembl-analysis/commits/cb60775b7569ff4485783c727816bd72bafae222"},{"sha":"173aa516cfdc8d0bf39d2f8903fde59636de9cb9","author":{"email":"aa5ef0a84f95a8b352d9bda81a0c8ef099dcb88a@ebi.ac.uk","name":"fergalmartin"},"message":"Created HiveLoadMitochondrion.pm\nAt the moment this is just a shell. Wanted to commit before pushing the branch","distinct":false,"url":"https://api.github.com/repos/Ensembl/ensembl-analysis/commits/173aa516cfdc8d0bf39d2f8903fde59636de9cb9"},{"sha":"20990fc51b619a2d37752f13ecc23929428e6188","author":{"email":"aa5ef0a84f95a8b352d9bda81a0c8ef099dcb88a@ebi.ac.uk","name":"fergalmartin"},"message":"Fixed HiveLoadMitochondrion.pm\nForgot to remove an unused variable when making module shell","distinct":false,"url":"https://api.github.com/repos/Ensembl/ensembl-analysis/commits/20990fc51b619a2d37752f13ecc23929428e6188"},{"sha":"f0d70fbd8e7accf3386068e1931f4d54e2b76488","author":{"email":"aa5ef0a84f95a8b352d9bda81a0c8ef099dcb88a@ebi.ac.uk","name":"fergalmartin"},"message":"Merge branch 'master' into dev/FAANG_hive_assembly_loading","distinct":false,"url":"https://api.github.com/repos/Ensembl/ensembl-analysis/commits/f0d70fbd8e7accf3386068e1931f4d54e2b76488"},{"sha":"db7723483fc8fdbbc8e6a467e96420032bb80c72","author":{"email":"aa5ef0a84f95a8b352d9bda81a0c8ef099dcb88a@ebi.ac.uk","name":"fergalmartin"},"message":"Change to HiveCreateDatabase\nAdded in code to run load_taxonomy script","distinct":false,"url":"https://api.github.com/repos/Ensembl/ensembl-analysis/commits/db7723483fc8fdbbc8e6a467e96420032bb80c72"},{"sha":"dc15997f757be5b3415a6f54f57b8c2a7d76f74b","author":{"email":"aa5ef0a84f95a8b352d9bda81a0c8ef099dcb88a@ebi.ac.uk","name":"fergalmartin"},"message":"Change to several modules in HiveAssemblyLoading\nChanged all the existing modules to use the eHive throw and warning implementations. Previously all modules were loading the core implementation of these and it was suggested that that would not function correctly with hive. All have now been changed to remove the use for the core implementation and call them both throw hive via","distinct":false,"url":"https://api.github.com/repos/Ensembl/ensembl-analysis/commits/dc15997f757be5b3415a6f54f57b8c2a7d76f74b"},{"sha":"6a81b9d4c6d7e63376b2b88a9defbea12aaa4635","author":{"email":"aa5ef0a84f95a8b352d9bda81a0c8ef099dcb88a@ebi.ac.uk","name":"fergalmartin"},"message":"Change to HiveCreateDatabase.pm\nAdded in taxon name flag to the module. If this and the taxon id are passed in it takes the taxon id over it","distinct":false,"url":"https://api.github.com/repos/Ensembl/ensembl-analysis/commits/6a81b9d4c6d7e63376b2b88a9defbea12aaa4635"},{"sha":"903542f4818f655bd6ff49b32f497f8ceb52f6cc","author":{"email":"aa5ef0a84f95a8b352d9bda81a0c8ef099dcb88a@ebi.ac.uk","name":"fergalmartin"},"message":"Merge branch 'dev/hive_master' into dev/FAANG_hive_assembly_loading","distinct":false,"url":"https://api.github.com/repos/Ensembl/ensembl-analysis/commits/903542f4818f655bd6ff49b32f497f8ceb52f6cc"}]}