File Changes for angie

v486_base to v487_preview (2025-08-11 to 2025-08-18) v487

• src/hg/hgTables/schema.c
  • lines changed 2, 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/hgTracks/hgTracks.h
  • lines changed 3, 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/hgTracks/loraxTrack.c
  • lines changed 100, 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/hgTracks/makefile
  • lines changed 1, 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/hgTracks/simpleTracks.c
  • lines changed 4, 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/hgc/hgc.c
  • lines changed 4, 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/hgc/hgc.h
  • lines changed 3, 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/hgc/loraxClick.c
  • lines changed 48, 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).
  • lines changed 2, 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/makefile
  • lines changed 1, 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/js/lorax.js
  • lines changed 8, 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/js/makefile
  • lines changed 1, 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/makeDb/trackDb/human/hg38/tgpArchive.ra
  • lines changed 12, 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).
  • lines changed 1, 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/makeDb/trackDb/tagTypes.tab
  • lines changed 4, 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).
  • lines changed 1, 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/utils/otto/dengue/buildTree.sh
  • lines changed 11, context: html, text, full: html, text
    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/fluA/buildConcatTree.sh
  • lines changed 22, 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/buildConcatTreeD1.1.sh
  • lines changed 320, 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/buildTree.sh
  • lines changed 112, 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/concat.config.json
  • lines changed 2, 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/genofluToSegmentMetadata.py
  • lines changed 58, 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/h5n1_ha.config.json
  • lines changed 5, 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/pb2.config.json
  • lines changed 5, 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/runGenoFlu.sh
  • lines changed 63, 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/updateAndersenLab.sh
  • lines changed 31, context: html, text, full: html, text
    236232f2b6c67b0ee2c39a9baa9480c9a500423f Tue Jun 3 09:27:37 2025 -0700
    Updated naming conventions
• src/hg/utils/otto/mpxv/buildTree.sh
  • lines changed 159, context: html, text, full: html, text
    f9ee0c7ea6540636411b7ff4a6ed54ab574701e2 Tue Jun 3 11:04:31 2025 -0700
    Add Clade I.
• src/hg/utils/otto/mpxv/getNcbiMpxv.sh
  • lines changed 33, context: html, text, full: html, text
    f9ee0c7ea6540636411b7ff4a6ed54ab574701e2 Tue Jun 3 11:04:31 2025 -0700
    Add Clade I.
• src/hg/utils/otto/mtb/buildTree.sh
  • lines changed 12, 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/getNcbiMtb.sh
  • lines changed 1, 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/taxonium.annotated.config.json
  • lines changed 93, 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/nextstrainNcov/doUpdate.sh
  • lines changed 2, 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/rsv/buildTree.sh
  • lines changed 61, 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/sarscov2phylo/extractPublicTree.sh
  • lines changed 32, 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/getCncb.sh
  • lines changed 3, 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/mapleMerge.py
  • lines changed 229, 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/nextstrain.clade-mutations.tsv
  • lines changed 2, 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/updateCombinedTree.sh
  • lines changed 2, 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/updateIdMapping.sh
  • lines changed 1, 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/updateLineageTreePb.sh
  • lines changed 54, 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/updatePublic.sh
  • lines changed 5, 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/vcfToMaple.py
  • lines changed 97, 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.