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Bulk: UCSC updates #50393

Merged
merged 4,265 commits into from
Aug 28, 2024
Merged

Bulk: UCSC updates #50393

merged 4,265 commits into from
Aug 28, 2024
This pull request is big! We’re only showing the most recent 250 commits.

Commits on Jun 12, 2024

  1. bulk fixes and failures

    @aliciaaevans
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  2. [ci run] trigger bulk run

    @aliciaaevans
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  3. [ci skip] add build failure record for recipe recipes/cgat-apps

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  4. [ci skip] fix pcaone openmp dependency

    @johanneskoester
    johanneskoester committed Jun 12, 2024
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  5. [ci skip] remove build failure record for recipe recipes/genometools-… 

    …genometools
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  6. [ci skip] add build failure record for recipe recipes/cgat-apps

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  7. [ci skip] add build failure record for recipe recipes/tobias

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  8. remove caching as it causes problems and doesn't save much time

    @aliciaaevans
    aliciaaevans committed Jun 12, 2024
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  9. move run_exports to correct location

    @aliciaaevans
    aliciaaevans committed Jun 12, 2024
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  10. add run_exports

    @aliciaaevans
    aliciaaevans committed Jun 12, 2024
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  11. rebuild failure

    @aliciaaevans
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  12. skiplist build failures

    @aliciaaevans
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  13. [ci run] trigger bulk run

    @aliciaaevans
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  14. [ci skip] add build failure record for recipe recipes/maxentpy

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  15. [ci skip] remove build failure record for recipe recipes/pcaone

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  16. [ci skip] add build failure record for recipe recipes/maxentpy

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  17. [ci skip] remove build failure record for recipe recipes/pcaone

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  18. [ci skip] add build failure record for recipe recipes/pydnase

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  19. [ci skip] add build failure record for recipe recipes/ntsynt

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  20. [ci skip] add build failure record for recipe recipes/nanovar

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  21. [ci skip] add build failure record for recipe recipes/chorus2

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  22. [ci skip] remove build failure record for recipe recipes/rpbp

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  23. bulk fixes and failures

    @aliciaaevans
    aliciaaevans committed Jun 12, 2024
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  24. [ci run] trigger bulk run

    @aliciaaevans
    aliciaaevans committed Jun 12, 2024
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  25. remove bad character

    @aliciaaevans
    aliciaaevans committed Jun 12, 2024
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  26. [ci skip] add build failure record for recipe recipes/chorus2

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  27. [ci skip] add build failure record for recipe recipes/whatshap

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  28. bulk fixes and failures

    @aliciaaevans
    aliciaaevans committed Jun 12, 2024
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  29. [ci run] trigger bulk run

    @aliciaaevans
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Commits on Jun 13, 2024

  1. exclude bioconda-repodata-patches

    @aliciaaevans
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  2. the other one is not the same

    @aliciaaevans
    aliciaaevans committed Jun 13, 2024
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  3. only run linux but add extra runners

    @aliciaaevans
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  4. [ci run] trigger bulk run

    @aliciaaevans
    aliciaaevans committed Jun 13, 2024
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  5. rebuild osx failures

    @aliciaaevans
    aliciaaevans committed Jun 13, 2024
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  6. revert runner changes

    @aliciaaevans
    aliciaaevans committed Jun 13, 2024
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  7. add run_exports

    @aliciaaevans
    aliciaaevans committed Jun 13, 2024
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  8. remove build failure

    @aliciaaevans
    aliciaaevans committed Jun 13, 2024
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  9. skiplist

    @aliciaaevans
    aliciaaevans committed Jun 13, 2024
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  10. [ci run] trigger bulk run

    @aliciaaevans
    aliciaaevans committed Jun 13, 2024
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  11. [ci skip] remove build failure record for recipe recipes/gsalign

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  12. [ci skip] remove build failure record for recipe recipes/bustools

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  13. [ci skip] remove build failure record for recipe recipes/metabuli

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  14. [ci skip] remove build failure record for recipe recipes/nonpareil

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  15. [ci skip] remove build failure record for recipe recipes/f5c

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  16. [ci skip] remove build failure record for recipe recipes/sankoff

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  17. [ci skip] remove build failure record for recipe recipes/humid

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  18. [ci skip] add build failure record for recipe recipes/pepsirf

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  19. [ci skip] remove build failure record for recipe recipes/flexiplex

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  20. [ci skip] remove build failure record for recipe recipes/gatb

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  21. [ci skip] remove build failure record for recipe recipes/stare-abc

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  22. [ci skip] remove build failure record for recipe recipes/encode-black… 

    …list
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  23. [ci skip] add build failure record for recipe recipes/phyloacc

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  24. [ci skip] remove build failure record for recipe recipes/parascopy

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  25. [ci skip] remove build failure record for recipe recipes/metagraph

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  26. [ci skip] remove build failure record for recipe recipes/msisensor-pro

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  27. [ci skip] add build failure record for recipe recipes/verifybamid2

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  28. [ci skip] remove build failure record for recipe recipes/ksnp

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  29. [ci skip] add build failure record for recipe recipes/ataqv

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  30. [ci skip] remove build failure record for recipe recipes/arriba

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  31. add run_exports

    @aliciaaevans
    aliciaaevans committed Jun 13, 2024
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  32. skip build failures

    @aliciaaevans
    aliciaaevans committed Jun 13, 2024
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  33. [ci run] trigger bulk run

    @aliciaaevans
    aliciaaevans committed Jun 13, 2024
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  34. [ci skip] remove build failure record for recipe recipes/scelestial

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  35. [ci skip] remove build failure record for recipe recipes/fastsimbac

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  36. Merge branch 'master' into bulk

    @aliciaaevans
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  37. [ci run] trigger bulk run

    @aliciaaevans
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  38. [ci skip] remove build failure record for recipe recipes/mgems

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  39. [ci skip] add build failure record for recipe recipes/mykrobe

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  40. [ci skip] add build failure record for recipe recipes/pegasuspy

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  41. [ci skip] add build failure record for recipe recipes/spades

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  42. [ci skip] remove build failure record for recipe recipes/jcvi

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  43. [ci skip] remove build failure record for recipe recipes/rpbp

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  44. [ci skip] add build failure record for recipe recipes/dicey

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  45. [ci skip] add build failure record for recipe recipes/zol

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  46. Merge branch 'master' into bulk

    @aliciaaevans
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  47. revert temporary CI changes

    @aliciaaevans
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  48. bump divergent build strings

    @aliciaaevans
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  49. skiplist build failures

    @aliciaaevans
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  50. [ci run] trigger bulk run

    @aliciaaevans
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  51. [ci skip] add build failure record for recipe recipes/dinopy

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  52. [ci skip] add build failure record for recipe recipes/dinopy

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  53. [ci skip] add build failure record for recipe recipes/dicey

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  54. [ci skip] remove build failure record for recipe recipes/tiddit

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  55. [ci skip] add build failure record for recipe recipes/dinopy

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  56. [ci skip] add build failure record for recipe recipes/phispy

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  57. [ci skip] add build failure record for recipe recipes/pyopal

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  58. [ci skip] add build failure record for recipe recipes/dicey

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  59. [ci skip] add build failure record for recipe recipes/zol

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Commits on Jun 14, 2024

  1. [ci skip] add build failure record for recipe recipes/pegasuspy

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  2. [ci skip] add build failure record for recipe recipes/bamread

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  3. skiplist build failures

    @aliciaaevans
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  4. Merge branch 'master' into bulk

    @aliciaaevans
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  5. bump build number

    @aliciaaevans
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  6. [ci run] trigger bulk run

    @aliciaaevans
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  7. [ci skip] add build failure record for recipe recipes/dinopy

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  8. [ci skip] add build failure record for recipe recipes/pegasuspy

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  9. [ci skip] add build failure record for recipe recipes/dinopy

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  10. [ci skip] add build failure record for recipe recipes/pegasuspy

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  11. bump updated recipes

    @aliciaaevans
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  12. centrifuge: add linux-aarch64 build (#48450) 

    * centrifuge: add linux-aarch64 build

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>

* Add a patch for fixing the build on linux aarch64

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>

---------

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>
    @martin-g @aliciaaevans
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  13. Update matchms to 0.26.4 (#48478)

    @BiocondaBot @aliciaaevans
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  14. r-spp: add linux-aarch64 build (#48467) 

    * r-spp: add linux-aarch64 build

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>

* Add run_exports. Use DESCRIPTION as a license file, although it is just mentioning it

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>

---------

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>
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  15. callerpp: add linux-aarch64 build (#48442) 

    * callerpp: add linux-aarch64 build

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>

* Allow signed char for Linux aarch64

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>

* Bump the version to 0.1.5

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>

---------

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>
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  16. genepop: add linux-aarch64 build (#48468) 

    * genepop: add linux-aarch64 build

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>

* Remove from the blacklist

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>

* Fix the source url to an existing one, pointing to R-genepop 1.2.2

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>

* Reset the build number to 0

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>

* Require C++ for the build

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>

* Use Github tag for v1.2.2. Fix the build

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>

* Improve the test to deal with the new interactive behavior of the program

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>

* Simplify the test. It seems `echo -e` does not work well at the CI systems

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>

---------

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>
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  17. velvet: add linux-aarch64 build (#48469) 

    Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>
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  18. Update earlgrey to 4.3.0 (#48477)

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  19. bump build number

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  20. skiplist failures

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  21. Update pybiolib to 1.1.2141 (#48479)

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  22. [ci run] trigger bulk run

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  25. bump build number for pinnings

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  28. skiplist

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  29. add run exports

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  30. bump build number

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  1. Merge branch 'master' into bulk

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  2. fix incorrectly merged files

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  3. remove extra spaces

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  4. bulk update latest ucsc version and fix failures

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  5. remove all ucsc from skiplist

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  58. temporarily disable osx on bulk

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  59. remove build failures for http errors

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  60. remove failures related to disk space

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  61. remove failures related to http

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  62. skiplist build failures

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  63. [ci run] trigger bulk run

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  78. [ci skip] add build failure record for recipe recipes/ucsc-estorient

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  79. [ci skip] add build failure record for recipe recipes/ucsc-liftup

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  80. [ci skip] add build failure record for recipe recipes/ucsc-genepredto… 

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  81. [ci skip] add build failure record for recipe recipes/ucsc-gff3togene… 

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  82. [ci skip] add build failure record for recipe recipes/ucsc-genepredto… 

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  83. [ci skip] add build failure record for recipe recipes/ucsc-genepredto… 

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  84. [ci skip] add build failure record for recipe recipes/ucsc-hgtrackdb

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  85. [ci skip] add build failure record for recipe recipes/ucsc-bamtopsl

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  86. [ci skip] add build failure record for recipe recipes/ucsc-transmapps… 

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  87. [ci skip] add build failure record for recipe recipes/ucsc-maffrags

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  88. [ci skip] add build failure record for recipe recipes/ucsc-rasqlquery

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  89. [ci skip] add build failure record for recipe recipes/ucsc-getrna

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  90. [ci skip] add build failure record for recipe recipes/ucsc-mafgene

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  91. [ci skip] add build failure record for recipe recipes/ucsc-featurebits

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  92. [ci skip] add build failure record for recipe recipes/ucsc-tdbquery

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  93. [ci skip] add build failure record for recipe recipes/ucsc-websync

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  94. [ci skip] add build failure record for recipe recipes/ucsc-mafsplitpos

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  95. [ci skip] add build failure record for recipe recipes/ucsc-maffrag

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  96. remove http errors

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  97. fix curly brackets

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  98. fix curly brackets

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  99. [ci run] trigger bulk run

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  100. [ci skip] add build failure record for recipe recipes/ucsc-bedjointab… 

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  101. [ci skip] add build failure record for recipe recipes/ucsc-genepredtobed

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  102. [ci skip] add build failure record for recipe recipes/ucsc-genepredto… 

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  103. [ci skip] add build failure record for recipe recipes/ucsc-gtftogenepred

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  104. [ci skip] add build failure record for recipe recipes/ucsc-hgloadchain

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  105. [ci skip] add build failure record for recipe recipes/ucsc-hgloadmaf

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  106. [ci skip] add build failure record for recipe recipes/ucsc-bedjointab… 

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  107. [ci skip] add build failure record for recipe recipes/ucsc-genepredcheck

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  108. [ci skip] add build failure record for recipe recipes/ucsc-gff3togene… 

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  109. [ci skip] add build failure record for recipe recipes/ucsc-mrnatogene

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  110. [ci skip] add build failure record for recipe recipes/ucsc-bedextendr… 

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  111. [ci skip] add build failure record for recipe recipes/ucsc-checkhgfin… 

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  112. skip failed builds

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  113. remove linux-aarch64 from known failures

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  114. [ci run] trigger bulk run

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  115. [ci skip] add build failure record for recipe recipes/ucsc-hgtrackdb

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  116. [ci skip] add build failure record for recipe recipes/ucsc-hubcheck

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Commits on Aug 28, 2024

  1. re-enable osx builds

    @aliciaaevans
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  2. Merge branch 'master' into bulk

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  3. [ci run] trigger bulk run

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  4. [ci skip] add build failure record for recipe recipes/ucsc-bigwigsummary

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  5. [ci skip] add build failure record for recipe recipes/sorted_nearest

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  6. [ci skip] add build failure record for recipe recipes/flye

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  7. merge script update and osx changes

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  8. skip broken osx-arm64 builds

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  9. Merge branch 'master' into bulk

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  10. [ci run] trigger bulk run

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  11. [ci skip] remove build failure record for recipe recipes/ucsc-bigwigs… 

    …ummary
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  12. remove accidental checkins

    @aliciaaevans
    aliciaaevans committed Aug 28, 2024
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