Commits for angie

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

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/getCogUk.sh - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/otto/sarscov2phylo/getNcbi.sh - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/otto/sarscov2phylo/gisaidFromChunks.sh - lines changed 2, context: html, text, full: html, text

50c3ab948546ac10a2f0bf151ab51c8b836bafd9 Mon Oct 4 16:58:39 2021 -0700

• Use normal priority for cluster run.
  • src/hg/utils/otto/sarscov2phylo/usherClusterRun.sh - lines changed 1, 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/extractPublicTree.sh - lines changed 2, context: html, text, full: html, text
  • src/hg/utils/otto/sarscov2phylo/makeNewMaskedVcf.sh - lines changed 11, context: html, text, full: html, text
  • src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh - lines changed 6, context: html, text, full: html, text

d8eaf7199fbe62ec8b6b565424306da70f571d99 Tue Oct 5 17:36:58 2021 -0700

• Don't forget the new hg/cgilib in the top-level libs and hgLib targets.
  • src/makefile - lines changed 1, context: html, text, full: html, text

4f684d9f3528f106c33c8f71f36629972d95fdeb Tue Oct 5 17:42:23 2021 -0700

• Forgot to check for NULL... always check for NULL. Always.
  • src/hg/hgPhyloPlace/phyloPlace.c - lines changed 1, context: html, text, full: html, text

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/hgPhyloPlace/phyloPlace.c - lines changed 7, 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/makeNewMaskedVcf.sh - lines changed 4, context: html, text, full: html, text
  • src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh - lines changed 4, context: html, text, full: html, text