File Changes for angie

v422_preview to v422_preview2 (2021-10-04 to 2021-10-11) v422

• src/hg/hgPhyloPlace/phyloPlace.c
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    4f684d9f3528f106c33c8f71f36629972d95fdeb Tue Oct 5 17:42:23 2021 -0700
    Forgot to check for NULL... always check for NULL. Always.
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    fde62c7a689e744c436c75ebc8dc7640b0800239 Wed Oct 6 09:16:49 2021 -0700
    Add a note that trash files will expire in 2 days and should be downloaded if intended for long-term use.
• src/hg/utils/otto/sarscov2phylo/extractPublicTree.sh
  • lines changed 2, context: html, text, full: html, text
    e931fd3e5fdab83eeb110b2450a0f365eff170e2 Mon Oct 4 17:04:17 2021 -0700
    Omit ORF1a from taxodium amino acid annotations (redundant with ORF1ab). Add optional baseProtobuf arg to updateCombinedTree.sh / makeNewMaskedVcf.sh to start with a custom protobuf (e.g. optimized) instead of eyesterday's protobuf.
• src/hg/utils/otto/sarscov2phylo/getCogUk.sh
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    4d34cfc382f4e45a7119129b2baa6a8645b80542 Fri Oct 1 14:21:27 2021 -0700
    Max pointed out that 8 threads would be much more reasonable for xz than 50.
• src/hg/utils/otto/sarscov2phylo/getNcbi.sh
  • lines changed 1, context: html, text, full: html, text
    4d34cfc382f4e45a7119129b2baa6a8645b80542 Fri Oct 1 14:21:27 2021 -0700
    Max pointed out that 8 threads would be much more reasonable for xz than 50.
• src/hg/utils/otto/sarscov2phylo/gisaidFromChunks.sh
  • lines changed 2, context: html, text, full: html, text
    4d34cfc382f4e45a7119129b2baa6a8645b80542 Fri Oct 1 14:21:27 2021 -0700
    Max pointed out that 8 threads would be much more reasonable for xz than 50.
• src/hg/utils/otto/sarscov2phylo/makeNewMaskedVcf.sh
  • lines changed 11, context: html, text, full: html, text
    e931fd3e5fdab83eeb110b2450a0f365eff170e2 Mon Oct 4 17:04:17 2021 -0700
    Omit ORF1a from taxodium amino acid annotations (redundant with ORF1ab). Add optional baseProtobuf arg to updateCombinedTree.sh / makeNewMaskedVcf.sh to start with a custom protobuf (e.g. optimized) instead of eyesterday's protobuf.
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    2bd08d43e884241b1e759bd87782e7bab62e1a5c Wed Oct 6 09:19:00 2021 -0700
    Oops, check more carefully for new optional arg.
• src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh
  • lines changed 6, context: html, text, full: html, text
    e931fd3e5fdab83eeb110b2450a0f365eff170e2 Mon Oct 4 17:04:17 2021 -0700
    Omit ORF1a from taxodium amino acid annotations (redundant with ORF1ab). Add optional baseProtobuf arg to updateCombinedTree.sh / makeNewMaskedVcf.sh to start with a custom protobuf (e.g. optimized) instead of eyesterday's protobuf.
  • lines changed 4, context: html, text, full: html, text
    2bd08d43e884241b1e759bd87782e7bab62e1a5c Wed Oct 6 09:19:00 2021 -0700
    Oops, check more carefully for new optional arg.
• src/hg/utils/otto/sarscov2phylo/usherClusterRun.sh
  • lines changed 1, context: html, text, full: html, text
    50c3ab948546ac10a2f0bf151ab51c8b836bafd9 Mon Oct 4 16:58:39 2021 -0700
    Use normal priority for cluster run.
• src/makefile
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    d8eaf7199fbe62ec8b6b565424306da70f571d99 Tue Oct 5 17:36:58 2021 -0700
    Don't forget the new hg/cgilib in the top-level libs and hgLib targets.