Commits for angie
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v486_base to v487_preview (2025-08-11 to 2025-08-18) v487
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da068f4b13595bfb45af25849abab4d89f816b5b Tue Jun 3 08:40:49 2025 -0700
- Reduce threads to avoid lockup in usher-sampled and matOptimize. Update hgdownload2 --> hgdownload3 and tolerate hgdownload rsync failure.
- src/hg/utils/otto/dengue/buildTree.sh - lines changed 11, context: html, text, full: html, text
1a144b066558c8c401c4440635f0f4aa68707806 Tue Jun 3 08:43:18 2025 -0700
- Reduce threads to avoid lockup in usher-sampled and matOptimize. Remove items with bogus dates to avoid crashing chronumental. Specify B3.13 because there's also D1.1. Update hgdownload2 --> hgdownload3 and tolerate hgdownload rsync failure.
- src/hg/utils/otto/fluA/buildConcatTree.sh - lines changed 22, context: html, text, full: html, text
63452d3fc64291c480595973b542b279d32dd256 Tue Jun 3 08:44:00 2025 -0700
- Concatenated-segment build for genotype D1.1.
- src/hg/utils/otto/fluA/buildConcatTreeD1.1.sh - lines changed 320, context: html, text, full: html, text
41e22d6a4bde0b7e897cb88724d4a27a14fe64e0 Tue Jun 3 09:26:25 2025 -0700
- Reduce threads to avoid lockup in usher-sampled and matOptimize. Add SRA assembly seqs to all segment builds. Pass VCF to matOptimize. Use cvstk to join with headers instead of complicated pipe. Add GenoFlu genotypes to metadata for H5N1. Update hgdownload2 --> hgdownload3 and tolerate hgdownload rsync failure.
- src/hg/utils/otto/fluA/buildTree.sh - lines changed 112, context: html, text, full: html, text
- src/hg/utils/otto/fluA/genofluToSegmentMetadata.py - lines changed 58, context: html, text, full: html, text
- src/hg/utils/otto/fluA/runGenoFlu.sh - lines changed 63, context: html, text, full: html, text
236232f2b6c67b0ee2c39a9baa9480c9a500423f Tue Jun 3 09:27:37 2025 -0700
- Updated naming conventions
- src/hg/utils/otto/fluA/updateAndersenLab.sh - lines changed 31, context: html, text, full: html, text
f01307d6c89f243afd4e0eafe0d4421fb05f6039 Tue Jun 3 09:28:38 2025 -0700
- Add genoflu types to metadata. Color by serotype by default.
- src/hg/utils/otto/fluA/h5n1_ha.config.json - lines changed 5, context: html, text, full: html, text
- src/hg/utils/otto/fluA/pb2.config.json - lines changed 5, context: html, text, full: html, text
643a144d0cd42d469fb6181b59ba89e95972cce2 Tue Jun 3 09:28:49 2025 -0700
- Color by host by default.
- src/hg/utils/otto/fluA/concat.config.json - lines changed 2, context: html, text, full: html, text
f9ee0c7ea6540636411b7ff4a6ed54ab574701e2 Tue Jun 3 11:04:31 2025 -0700
- Add Clade I.
- src/hg/utils/otto/mpxv/buildTree.sh - lines changed 159, context: html, text, full: html, text
- src/hg/utils/otto/mpxv/getNcbiMpxv.sh - lines changed 33, context: html, text, full: html, text
5af316b0f05735ba8dfb8a8264fe634e16e5bb22 Tue Jun 3 11:07:21 2025 -0700
- Reduce threads to avoid lockup in usher-sampled and matOptimize. Remove Goya clades because they were removed from nextclade. Update hgdownload2 --> hgdownload3 and tolerate hgdownload rsync failure.
- src/hg/utils/otto/rsv/buildTree.sh - lines changed 61, context: html, text, full: html, text
8a0ebbbae627da20c8c7c65aa57d297e5a19529a Tue Jun 3 11:08:52 2025 -0700
- Tweak download dir name. Update hgdownload2 --> hgdownload3 and tolerate hgdownload rsync failure.
- src/hg/utils/otto/mtb/buildTree.sh - lines changed 12, context: html, text, full: html, text
- src/hg/utils/otto/mtb/getNcbiMtb.sh - lines changed 1, context: html, text, full: html, text
47df01a42e26269a5c952013a35cb5633e3c0f45 Tue Jun 3 11:10:06 2025 -0700
- Check for existence of bedGraph file before running bedGraphToBigWig.
- src/hg/utils/otto/nextstrainNcov/doUpdate.sh - lines changed 2, context: html, text, full: html, text
ca72f8065c8d796eeaaa43955bde1c6dc2ce9487 Tue Jun 3 11:13:18 2025 -0700
- Maple utility scripts for merging in N bases from VCF files to maple dumped from UShER tree. This was for Nicola de Maio to run SPRTA on the UShER tree with merged MAPLE or reviewer comments on viridian tree manuscript.
- src/hg/utils/otto/sarscov2phylo/mapleMerge.py - lines changed 229, context: html, text, full: html, text
- src/hg/utils/otto/sarscov2phylo/vcfToMaple.py - lines changed 97, context: html, text, full: html, text
9012336f7d4569de36ea47886405c770b23a1ea1 Tue Jun 3 11:15:43 2025 -0700
- CNCB apparently shut down access so just use last downloaded set.
- src/hg/utils/otto/sarscov2phylo/updateIdMapping.sh - lines changed 1, context: html, text, full: html, text
22d7aeffdf9fcd45a7ec9acf96c57eafdd55b218 Tue Jun 3 11:16:28 2025 -0700
- tweak CGI-encoding of metadataUrl... to no avail, they seem to have shut down access.
- src/hg/utils/otto/sarscov2phylo/getCncb.sh - lines changed 3, context: html, text, full: html, text
65e3f367ddcc011118e795f0b8623058051d4c43 Tue Jun 3 11:18:27 2025 -0700
- Compress Newick download file (as should have done from the beginning). Remove MSA download, it's flawed and apparently unused.
- src/hg/utils/otto/sarscov2phylo/extractPublicTree.sh - lines changed 32, context: html, text, full: html, text
2ece0f9519a3322fec8ecb7a283645b2c690b337 Tue Jun 3 11:19:26 2025 -0700
- Added new clades 25A (LP.8.1) and 25B (NB.1.8.1).
- src/hg/utils/otto/sarscov2phylo/nextstrain.clade-mutations.tsv - lines changed 2, context: html, text, full: html, text
ed655b70beb98c16d99689a1485b511d0b27d408 Tue Jun 3 11:20:34 2025 -0700
- Tolerate updateIdMapping.sh failure (always caused by download failure) and let build proceed with latest available mapping.
- src/hg/utils/otto/sarscov2phylo/updatePublic.sh - lines changed 5, context: html, text, full: html, text
3da34ac26ab54ab67a772579de61222237f99e85 Tue Jun 3 11:22:08 2025 -0700
- Exempt a couple lineages with few representatives, all of which have reversions, from the reversion-pruner. Update to use .pb.gz instead of .pb.
- src/hg/utils/otto/sarscov2phylo/updateLineageTreePb.sh - lines changed 54, context: html, text, full: html, text
9ae312b796eca29cd110e08ecc8506ca593fcbfd Tue Jun 3 11:22:47 2025 -0700
- Relax branch length filter again (for BA.3.2).
- src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh - lines changed 2, context: html, text, full: html, text
ba10a7b1b7fae45ac511702425528670042b8c9f Tue Jun 3 11:26:10 2025 -0700
- Taxonium config file for SRA Mtb tree with Ash's ranchero metadata.
- src/hg/utils/otto/mtb/taxonium.annotated.config.json - lines changed 93, context: html, text, full: html, text
5a34c495d5fe1db2aab6d1785c0b0239dbed2520 Sat Aug 16 21:21:02 2025 -0700
- New track type lorax: details page embeds Lorax multi-tree viewer.
The trees are subtrees of an Ancestral Recombination Graph (ARG).
This commit also adds a track with 1000 Genomes data, tgpLorax.
The details page uses an iframe to embed the Lorax viewer from
a separate server (most likely will run in a docker container on
the GB server hosts; that will make this track more complicated for
mirror operators than other tracks).
- src/hg/hgTables/schema.c - lines changed 2, context: html, text, full: html, text
- src/hg/hgTracks/hgTracks.h - lines changed 3, context: html, text, full: html, text
- src/hg/hgTracks/loraxTrack.c - lines changed 100, context: html, text, full: html, text
- src/hg/hgTracks/makefile - lines changed 1, context: html, text, full: html, text
- src/hg/hgTracks/simpleTracks.c - lines changed 4, context: html, text, full: html, text
- src/hg/hgc/loraxClick.c - lines changed 48, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/tgpArchive.ra - lines changed 12, context: html, text, full: html, text
- src/hg/makeDb/trackDb/tagTypes.tab - lines changed 4, context: html, text, full: html, text
fca649f40a04767fbd9c331ef4e4b37f25882bf0 Mon Aug 18 09:16:01 2025 -0700
- Changing tdb setting name from loraxBackendUrl (misnomer) to loraxIframeUrlBase.
- src/hg/hgc/loraxClick.c - lines changed 2, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/tgpArchive.ra - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/tagTypes.tab - lines changed 1, context: html, text, full: html, text
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