Paige Kulzer added a comment - 12/Sep/24 2:04 PM Current UCSC API genomes: https://api.genome.ucsc.edu/list/ucscGenomes "caePb1": { "description": "Jan. 2007 (WUGSC 4.0/caePb1)", "nibPath": "/gbdb/caePb1", "organism": "C. brenneri", "defaultPos": "chrUn:97956213-97960870", "active": 1, "orderKey": 3012, "genome": "C. brenneri", "scientificName": "Caenorhabditis brenneri", "htmlPath": "/gbdb/caePb1/html/description.html", "hgNearOk": 0, "hgPbOk": 0, "sourceName": "Washington University School of Medicine GSC Caenorhabditis n. sp. PB2801", "taxId": 135651 }, "caePb2": { "description": "Feb. 2008 (WUGSC 6.0.1/caePb2)", "nibPath": "/gbdb/caePb2", "organism": "C. brenneri", "defaultPos": "chrUn:117559143-117563800", "active": 1, "orderKey": 3011, "genome": "C. brenneri", "scientificName": "Caenorhabditis brenneri", "htmlPath": "/gbdb/caePb2/html/description.html", "hgNearOk": 0, "hgPbOk": 0, "sourceName": "Washington University School of Medicine GSC Caenorhabditis brenneri (PB2801) 6.0.1", "taxId": 135651 } "hs1": { "description": "Jan. 2022 (T2T CHM13v2.0/hs1)", "nibPath": "hub:/gbdb/hs1/hubs", "organism": "Human", "defaultPos": "chr9:145458455-145495201", "active": 1, "orderKey": 45, "genome": "Human", "scientificName": "Homo sapiens", "htmlPath": "/gbdb/hs1/html/description.html", "hgNearOk": 0, "hgPbOk": 0, "sourceName": "Telomere to telomere (T2T) assembly of haploid CHM13 + chrY (GCA_009914755.4)", "taxId": 9606 } "mpxvRivers": { "description": "MPXV-M5312_HM12_Rivers (MT903340.1/GCF_014621545.1)", "nibPath": "hub:/gbdb/mpxvRivers/hubs", "organism": "Monkeypox virus", "defaultPos": "NC_063383.1:65,736-75,736", "active": 1, "orderKey": 22325, "genome": "Monkeypox virus", "scientificName": "Monkeypox virus", "htmlPath": "/gbdb/mpxvRivers/html/description.html", "hgNearOk": 0, "hgPbOk": 1, "sourceName": "Monkeypox virus", "taxId": 10244 }

Paige Kulzer added a comment - 12/Sep/24 2:26 PM - edited The hs and mpxvRivers genomes are currently not listed in either synonyms.txt or species.txt (from the IGB code base) which is what has caused this issue. The caePb genome is currently listed and seemingly formatted correctly in both, so will need further investigation why that specific genome name is being displayed. For example, please see attached for two images: 1) an image of what the human genome (hs) is currently listed as in the drop-down menu (hs.png), and 2) an image of what the human genome was listed as after the addition of this genome to both synonyms.txt and species.txt (Homo sapiens.png).

Nowlan Freese added a comment - 12/Sep/24 3:28 PM Branch: https://bitbucket.org/nfreese/nowlanfork-igb/branch/IGBF-3902 Note: The issue with caePb was that there were two spaces instead of a tab character in the species.txt file, and this was causing the issue.

Paige Kulzer added a comment - 13/Sep/24 8:38 AM Changes and commit look good. Ready for pull request.

Nowlan Freese added a comment - 13/Sep/24 10:02 AM PR: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/1034

Ann Loraine added a comment - 13/Sep/24 4:51 PM - edited PR is merged and installers are built and copied to "Early Access" section of bioviz.org.

Paige Kulzer added a comment - 16/Sep/24 8:19 AM caePb/Caenorhabditis brenneri: No issues found with either of the two versions. The genome and genome versions are displaying correctly in the dropdown menus. Gene predictions loaded successfully, no errors in the Log. hs/Homo sapiens: No issues found. Clicking on the human image in the carousel now opens this version of the human genome. Also, the genome and genome version names in the drop down menus, as well as the synonyms that appear when hovering over the genome name in the drop down menu, all look correct. Gene models loaded on all of the numbered chromosomes, no errors in the Log. mpxvRivers/Monkeypox Virus: No issues found. The genome and genome versions are displaying correctly in the dropdown menus. Gene predictions loaded successfully, no errors in the Log. Everything looks fixed, closing this ticket!