Commits for hiram

v473_base to v474_preview (2024-10-28 to 2024-11-04) v474

e69db257480ddc4aae24ca6ae0130c9450abc362 Mon Oct 28 14:07:47 2024 -0700

• do not use /dev/shm as a temporary directory refs #34685
  • src/hg/utils/automation/HgAutomate.pm - lines changed 21, context: html, text, full: html, text
  • src/hg/utils/automation/doAugustus.pl - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/automation/doBlastzChainNet.pl - lines changed 8, context: html, text, full: html, text
  • src/hg/utils/automation/doCpgIslands.pl - lines changed 8, context: html, text, full: html, text
  • src/hg/utils/automation/doRepeatMasker.pl - lines changed 8, context: html, text, full: html, text
  • src/hg/utils/automation/doSameSpeciesLiftOver.pl - lines changed 2, context: html, text, full: html, text
  • src/hg/utils/automation/doSimpleRepeat.pl - lines changed 16, context: html, text, full: html, text
  • src/hg/utils/automation/doWindowMasker.pl - lines changed 16, context: html, text, full: html, text

27300d62d155d9941c226a2c27f3a33b3ea53ed0 Mon Oct 28 14:15:17 2024 -0700

• do not use /dev/shm as a temporary directory refs #34685
  • src/hg/utils/automation/asmHubRepeatMasker.sh - lines changed 8, context: html, text, full: html, text

2c6090e8d56e6c6ebf9fe8b1e348713451212743 Mon Oct 28 14:25:14 2024 -0700

• remember to remove the temporary seqList file from /dev/shm refs #34685
  • src/hg/utils/automation/doAssemblyHub.pl - lines changed 3, context: html, text, full: html, text

0fb5e02c75ed9836aecfb3a36987bfb8b5fd73e4 Mon Oct 28 19:37:36 2024 -0700

• temporary set doAugustus to cluster ku until hgcompute issues worked out refs #34685
  • src/hg/utils/automation/doAssemblyHub.pl - lines changed 2, context: html, text, full: html, text

5bd057d435611f90f3767e1c5bc9a73a56b62e8b Mon Oct 28 21:11:14 2024 -0700

• adding ram and cpu arguments since this process can work in 4gb with 1cpu refs #34685
  • src/hg/utils/automation/doSimpleRepeat.pl - lines changed 6, context: html, text, full: html, text

039188978e9faef534235afda7eb14aee6d6cda9 Tue Oct 29 14:00:02 2024 -0700

• handle the case of empty grep result on part.list refs #34685
  • src/hg/utils/automation/doCpgIslands.pl - lines changed 1, context: html, text, full: html, text

0c126bf17c586c00c15714a69ce874c1423e774f Tue Oct 29 14:56:19 2024 -0700

• indicate which paraHub the cluster job is on refs #34685
  • src/hg/utils/automation/doAugustus.pl - lines changed 1, context: html, text, full: html, text

2e584a1c66bae4339bd009372f47e97f0636fe85 Tue Oct 29 15:01:41 2024 -0700

• indicate which paraHub the cluster job is on refs #34685
  • src/hg/utils/automation/doRepeatMasker.pl - lines changed 1, context: html, text, full: html, text

dac1dd5605a7a3a9dab41ef36b3859953c454ad2 Tue Oct 29 15:03:43 2024 -0700

• indicate which paraHub the cluster job is on refs #34685
  • src/hg/utils/automation/doRepeatModeler.pl - lines changed 1, context: html, text, full: html, text

7b95c46185395e1500ab3a56bd185a11be4b9517 Wed Oct 30 21:17:55 2024 -0700

• not a good idea to use /tmp/ for the simple repeat - that filesystem is way too small for the long running hippos refs #34685
  • src/hg/utils/automation/doSimpleRepeat.pl - lines changed 16, context: html, text, full: html, text

767f1be1b487090edbfa9d3653af4a3192b81b7d Thu Oct 31 15:36:28 2024 -0700

• mistaken bash code in csh script refs #3468
  • src/hg/utils/automation/doBlastzChainNet.pl - lines changed 7, context: html, text, full: html, text

3bda44abd31a4cb5c19f7d6c0f66d6279bdf4cb7 Fri Nov 1 19:50:21 2024 -0700

• running an update for VGP refs #29545
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 58, context: html, text, full: html, text
  • src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv - lines changed 53, context: html, text, full: html, text
  • src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv - lines changed 20, context: html, text, full: html, text

e9d9c5ac5a0eb1a070918f2a261cf075e1dea1d2 Fri Nov 1 19:51:52 2024 -0700

• running an update for VGP refs #29545
  • src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv - lines changed 16, context: html, text, full: html, text

42d19c5cec90202c2b8f520de948905af057fe4e Sun Nov 3 13:07:26 2024 -0800

• switch from counting in genomes.txt and instead use the assemblyList.json and count up clades correctly refs #29545
  • src/hg/makeDb/doc/asmHubs/asmHubList.pl - lines changed 61, context: html, text, full: html, text
  • src/hg/makeDb/doc/asmHubs/hubIndex.pl - lines changed 8, context: html, text, full: html, text

7592170a1f176f724492f264eff0e094cc0bc316 Mon Nov 4 03:54:26 2024 -0800

• upgrade augustus binary and correct use of mktemp refs #34685
  • src/hg/utils/automation/doAssemblyHub.pl - lines changed 2, context: html, text, full: html, text
  • src/hg/utils/automation/doAugustus.pl - lines changed 20, context: html, text, full: html, text