Bulk: UCSC updates

.github/workflows/Bulk.yml

@@ -128,9 +128,9 @@ jobs:
     runs-on: macOS-14 # M1
     strategy:
       fail-fast: false
-      max-parallel: 4
+      max-parallel: 1 # GHA free plan allows 5 concurrent Mac runners total, we still need most on osx-64.
       matrix:
-        runner: [0, 1, 2, 3]
+        runner: [0]
     steps:
       - uses: actions/checkout@v4
         with:
@@ -179,7 +179,7 @@ jobs:
           python -c 'import bioconda_utils.utils as u ; import pathlib as p ; print(*(f"{f}:\n{p.Path(f).read_text()}" for f in u.load_conda_build_config().exclusive_config_files), sep="\n")'
           echo '============'
           bioconda-utils build recipes config.yml \
-            --worker-offset ${{ matrix.runner }} --n-workers 4 \
+            --worker-offset ${{ matrix.runner }} --n-workers 1 \
             --lint --anaconda-upload --record-build-failures --skiplist-leafs \
             --exclude bioconda-repodata-patches
           conda clean -y --all

build-fail-blacklist

@@ -632,10 +632,6 @@ recipes/tedna
 recipes/transtermhp
 recipes/carna
 
-# stringify can't find libmysqlclient.18
-recipes/ucsc-overlapselect
-recipes/ucsc-pslmap
-
 # Source seems to have moved
 recipes/discovar
 
@@ -760,202 +756,6 @@ recipes/maker
 # Takes hours to solve the environment
 recipes/rop
 
-# Need to redo the skeletons for these
-recipes/ucsc-axttomaf
-recipes/ucsc-bamtopsl
-recipes/ucsc-bedcoverage
-recipes/ucsc-bedextendranges
-recipes/ucsc-bedintersect
-recipes/ucsc-beditemoverlapcount
-recipes/ucsc-bedjointaboffset
-recipes/ucsc-bedpileups
-recipes/ucsc-bedrestricttopositions
-recipes/ucsc-bedtopsl
-recipes/ucsc-bedweedoverlapping
-recipes/ucsc-blasttopsl
-recipes/ucsc-catdir
-recipes/ucsc-catuncomment
-recipes/ucsc-chainbridge
-recipes/ucsc-chainfilter
-recipes/ucsc-chainnet
-recipes/ucsc-chainprenet
-recipes/ucsc-chainsplit
-recipes/ucsc-chainstitchid
-recipes/ucsc-chainswap
-recipes/ucsc-chaintoaxt
-recipes/ucsc-chaintopsl
-recipes/ucsc-chaintopslbasic
-recipes/ucsc-checkagpandfa
-recipes/ucsc-checkcoveragegaps
-recipes/ucsc-checkhgfindspec
-recipes/ucsc-checktablecoords
-recipes/ucsc-chopfalines
-recipes/ucsc-chromgraphfrombin
-recipes/ucsc-chromgraphtobin
-recipes/ucsc-clustergenes
-recipes/ucsc-coltransform
-recipes/ucsc-countchars
-recipes/ucsc-crtreeindexbed
-recipes/ucsc-crtreesearchbed
-recipes/ucsc-dbsnoop
-recipes/ucsc-dbtrash
-recipes/ucsc-endsinlf
-recipes/ucsc-estorient
-recipes/ucsc-expmatrixtobarchartbed
-recipes/ucsc-faalign
-recipes/ucsc-facmp
-recipes/ucsc-facount
-recipes/ucsc-fafilter
-recipes/ucsc-fafiltern
-recipes/ucsc-fafrag
-recipes/ucsc-fanoise
-recipes/ucsc-faonerecord
-recipes/ucsc-fapolyasizes
-recipes/ucsc-farandomize
-recipes/ucsc-farc
-recipes/ucsc-fasize
-recipes/ucsc-fasplit
-recipes/ucsc-fastqstatsandsubsample
-recipes/ucsc-fastqtofa
-recipes/ucsc-fatofastq
-recipes/ucsc-fatotab
-recipes/ucsc-fatrans
-recipes/ucsc-featurebits
-recipes/ucsc-findmotif
-recipes/ucsc-gaptolift
-recipes/ucsc-genepredfilter
-recipes/ucsc-genepredhisto
-recipes/ucsc-genepredsinglecover
-recipes/ucsc-genepredtofakepsl
-recipes/ucsc-genepredtomafframes
-recipes/ucsc-genepredtoprot
-recipes/ucsc-gensub2
-recipes/ucsc-getrna
-recipes/ucsc-getrnapred
-recipes/ucsc-gff3topsl
-recipes/ucsc-gmtime
-recipes/ucsc-headrest
-recipes/ucsc-hgbbidblink
-recipes/ucsc-hgfakeagp
-recipes/ucsc-hgfindspec
-recipes/ucsc-hggoldgapgl
-recipes/ucsc-hgloadbed
-recipes/ucsc-hgloadchain
-recipes/ucsc-hgloadmaf
-recipes/ucsc-hgloadnet
-recipes/ucsc-hgloadout
-recipes/ucsc-hgloadoutjoined
-recipes/ucsc-hgloadsqltab
-recipes/ucsc-hgloadwiggle
-recipes/ucsc-hgspeciesrna
-recipes/ucsc-hgsqldump
-recipes/ucsc-hgtrackdb
-recipes/ucsc-hgvstovcf
-recipes/ucsc-htmlcheck
-recipes/ucsc-hubcheck
-recipes/ucsc-hubpubliccheck
-recipes/ucsc-lavtoaxt
-recipes/ucsc-lavtopsl
-recipes/ucsc-ldhggene
-recipes/ucsc-liftup
-recipes/ucsc-linestora
-recipes/ucsc-localtime
-recipes/ucsc-mafaddirows
-recipes/ucsc-mafaddqrows
-recipes/ucsc-mafcoverage
-recipes/ucsc-maffetch
-recipes/ucsc-maffilter
-recipes/ucsc-maffrag
-recipes/ucsc-maffrags
-recipes/ucsc-mafgene
-recipes/ucsc-mafmefirst
-recipes/ucsc-maforder
-recipes/ucsc-mafranges
-recipes/ucsc-mafsinregion
-recipes/ucsc-mafspecieslist
-recipes/ucsc-mafspeciessubset
-recipes/ucsc-mafsplit
-recipes/ucsc-mafsplitpos
-recipes/ucsc-maftoaxt
-recipes/ucsc-maftobigmaf
-recipes/ucsc-maftopsl
-recipes/ucsc-maftosnpbed
-recipes/ucsc-maketablelist
-recipes/ucsc-maskoutfa
-recipes/ucsc-mktime
-recipes/ucsc-mrnatogene
-recipes/ucsc-netchainsubset
-recipes/ucsc-netclass
-recipes/ucsc-netfilter
-recipes/ucsc-netsplit
-recipes/ucsc-netsyntenic
-recipes/ucsc-nettoaxt
-recipes/ucsc-nettobed
-recipes/ucsc-newprog
-recipes/ucsc-newpythonprog
-recipes/ucsc-nibsize
-recipes/ucsc-overlapselect
-recipes/ucsc-para
-recipes/ucsc-parafetch
-recipes/ucsc-parahub
-recipes/ucsc-parahubstop
-recipes/ucsc-paranode
-recipes/ucsc-paranodestart
-recipes/ucsc-paranodestatus
-recipes/ucsc-paranodestop
-recipes/ucsc-parasol
-recipes/ucsc-parasync
-recipes/ucsc-paratestjob
-recipes/ucsc-positionaltblcheck
-recipes/ucsc-pslcat
-recipes/ucsc-pslcheck
-recipes/ucsc-psldropoverlap
-recipes/ucsc-pslfilter
-recipes/ucsc-pslliftsubrangeblat
-recipes/ucsc-pslmap
-recipes/ucsc-pslmappostchain
-recipes/ucsc-pslpartition
-recipes/ucsc-pslpretty
-recipes/ucsc-pslrc
-recipes/ucsc-pslreps
-recipes/ucsc-pslscore
-recipes/ucsc-pslselect
-recipes/ucsc-pslsomerecords
-recipes/ucsc-pslstats
-recipes/ucsc-pslswap
-recipes/ucsc-psltobigpsl
-recipes/ucsc-psltopslx
-recipes/ucsc-pslxtofa
-recipes/ucsc-qacagplift
-recipes/ucsc-qactoqa
-recipes/ucsc-qatoqac
-recipes/ucsc-randomlines
-recipes/ucsc-rasqlquery
-recipes/ucsc-ratolines
-recipes/ucsc-ratotab
-recipes/ucsc-rmfadups
-recipes/ucsc-rowstocols
-recipes/ucsc-spacedtotab
-recipes/ucsc-splitfile
-recipes/ucsc-splitfilebycolumn
-recipes/ucsc-sqltoxml
-recipes/ucsc-subcolumn
-recipes/ucsc-taillines
-recipes/ucsc-tdbquery
-recipes/ucsc-texthistogram
-recipes/ucsc-ticktodate
-recipes/ucsc-toupper
-recipes/ucsc-transmappsltogenepred
-recipes/ucsc-trfbig
-recipes/ucsc-twobitdup
-recipes/ucsc-twobitmask
-recipes/ucsc-validatefiles
-recipes/ucsc-validatemanifest
-recipes/ucsc-websync
-recipes/ucsc-wigcorrelate
-recipes/ucsc-wordline
-recipes/ucsc-xmltosql
-
 # Above v1.0.5 there are licensing restrictions and it cannot be distributed
 # via bioconda. See https://github.com/bioconda/bioconda-recipes/pull/23476.
 recipes/fishtaco

recipes/flye/build_failure.osx-arm64.yaml

@@ -0,0 +1,104 @@
+recipe_sha: 172c692d9e3bfbb5893c55d2f193b4bf7850c328e906cbd3c7b3328854b86677  # The hash of the recipe's meta.yaml at which this recipe failed to build.
+skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above.
+log: |2-
+
+    changing mode of $PREFIX/bin/flye to 755
+  Successfully installed flye-2.9.5
+  Removed build tracker: '/private/tmp/pip-build-tracker-h4l5mldh'
+
+  Resource usage statistics from building flye:
+     Process count: 12
+     CPU time: Sys=0:00:02.8, User=0:00:52.1
+     Memory: 1008.4M
+     Disk usage: 371.8K
+     Time elapsed: 0:00:44.4
+
+
+  Packaging flye
+  Packaging flye-2.9.5-py312h321ceac_0
+  /opt/mambaforge/envs/bioconda/conda-bld/flye_1724856988454/_build_env/bin/arm64-apple-darwin20.0.0-install_name_tool: warning: changes being made to the file will invalidate the code signature in: /opt/mambaforge/envs/bioconda/conda-bld/flye_1724856988454/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/bin/flye-samtools
+  [cctools-port]: generating fake signature for '/opt/mambaforge/envs/bioconda/conda-bld/flye_1724856988454/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/bin/flye-samtools'
+
+  /opt/mambaforge/envs/bioconda/conda-bld/flye_1724856988454/_build_env/bin/arm64-apple-darwin20.0.0-install_name_tool: warning: changes being made to the file will invalidate the code signature in: /opt/mambaforge/envs/bioconda/conda-bld/flye_1724856988454/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/bin/flye-samtools
+  [cctools-port]: generating fake signature for '/opt/mambaforge/envs/bioconda/conda-bld/flye_1724856988454/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/bin/flye-samtools'
+
+  /opt/mambaforge/envs/bioconda/conda-bld/flye_1724856988454/_build_env/bin/arm64-apple-darwin20.0.0-install_name_tool: warning: changes being made to the file will invalidate the code signature in: /opt/mambaforge/envs/bioconda/conda-bld/flye_1724856988454/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/bin/flye-samtools
+  [cctools-port]: generating fake signature for '/opt/mambaforge/envs/bioconda/conda-bld/flye_1724856988454/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/bin/flye-samtools'
+
+  /opt/mambaforge/envs/bioconda/conda-bld/flye_1724856988454/_build_env/bin/arm64-apple-darwin20.0.0-install_name_tool: warning: changes being made to the file will invalidate the code signature in: /opt/mambaforge/envs/bioconda/conda-bld/flye_1724856988454/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/bin/flye-minimap2
+  [cctools-port]: generating fake signature for '/opt/mambaforge/envs/bioconda/conda-bld/flye_1724856988454/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/bin/flye-minimap2'
+
+  /opt/mambaforge/envs/bioconda/conda-bld/flye_1724856988454/_build_env/bin/arm64-apple-darwin20.0.0-install_name_tool: warning: changes being made to the file will invalidate the code signature in: /opt/mambaforge/envs/bioconda/conda-bld/flye_1724856988454/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/bin/flye-modules
+  [cctools-port]: generating fake signature for '/opt/mambaforge/envs/bioconda/conda-bld/flye_1724856988454/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/bin/flye-modules'
+
+  /opt/mambaforge/envs/bioconda/conda-bld/flye_1724856988454/_build_env/bin/arm64-apple-darwin20.0.0-install_name_tool: warning: changes being made to the file will invalidate the code signature in: /opt/mambaforge/envs/bioconda/conda-bld/flye_1724856988454/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/bin/flye-modules
+  [cctools-port]: generating fake signature for '/opt/mambaforge/envs/bioconda/conda-bld/flye_1724856988454/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/bin/flye-modules'
+
+  WARNING: Importing conda-verify failed.  Please be sure to test your packages.  conda install conda-verify to make this message go away.
+  compiling .pyc files...
+  number of files: 104
+     INFO: sysroot: '/System/Library/Frameworks/' files: '['vmnet.framework/Versions/Current', 'vmnet.framework/Versions/A/_CodeSignature/CodeResources', 'vmnet.framework/Versions/A/Resources/version.plist', 'vmnet.framework/Versions/A/Resources/InfoPlist.loctable']'
+     INFO: sysroot: '/usr/lib/' files: '['zsh/5.9/zsh/zselect.so', 'zsh/5.9/zsh/zpty.so', 'zsh/5.9/zsh/zprof.so', 'zsh/5.9/zsh/zleparameter.so']'
+     INFO: sysroot: '/opt/X11/' files: '[]'
+     INFO (flye,bin/flye-samtools): Needed DSO lib/libz.1.dylib found in conda-forge/osx-arm64::libzlib==1.2.13=hfb2fe0b_6
+     INFO (flye,bin/flye-samtools): Needed DSO /System/Library/Frameworks/libSystem.B.dylib found in $SYSROOT
+     INFO (flye,bin/flye-minimap2): Needed DSO /System/Library/Frameworks/libSystem.B.dylib found in $SYSROOT
+     INFO (flye,bin/flye-minimap2): Needed DSO lib/libz.1.dylib found in conda-forge/osx-arm64::libzlib==1.2.13=hfb2fe0b_6
+     INFO (flye,bin/flye-modules): Needed DSO lib/libz.1.dylib found in conda-forge/osx-arm64::libzlib==1.2.13=hfb2fe0b_6
+     INFO (flye,bin/flye-modules): Needed DSO lib/libc.1.dylib found in conda-forge/osx-arm64::libcxx==18.1.8=h3ed4263_6
+     INFO (flye,bin/flye-modules): Needed DSO /System/Library/Frameworks/libSystem.B.dylib found in $SYSROOT
+     INFO (flye): Interpreted package 'flye' is interpreted by 'python'
+  Fixing permissions
+  Packaged license file/s.
+  INFO :: Time taken to mark (prefix)
+          0 replacements in 0 files was 0.07 seconds
+  Files containing CONDA_PREFIX
+  -----------------------------
+  bin/flye (text): Patching
+  TEST START: /opt/mambaforge/envs/bioconda/conda-bld/osx-arm64/flye-2.9.5-py312h321ceac_0.tar.bz2
+  Renaming work directory '/opt/mambaforge/envs/bioconda/conda-bld/flye_1724856988454/work' to '/opt/mambaforge/envs/bioconda/conda-bld/flye_1724856988454/work_moved_flye-2.9.5-py312h321ceac_0_osx-arm64'
+  shutil.move(work)=/opt/mambaforge/envs/bioconda/conda-bld/flye_1724856988454/work, dest=/opt/mambaforge/envs/bioconda/conda-bld/flye_1724856988454/work_moved_flye-2.9.5-py312h321ceac_0_osx-arm64)
+  Reloading output folder (local): ...working... done
+  Solving environment (_test_env): ...working... done
+
+  ## Package Plan ##
+
+    environment location: /opt/mambaforge/envs/bioconda/conda-bld/flye_1724856988454/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac
+
+
+  The following NEW packages will be INSTALLED:
+
+      bzip2:           1.0.8-h99b78c6_7          conda-forge
+      ca-certificates: 2024.7.4-hf0a4a13_0       conda-forge
+      flye:            2.9.5-py312h321ceac_0     local
+      libcxx:          18.1.8-h3ed4263_6         conda-forge
+      libexpat:        2.6.2-hebf3989_0          conda-forge
+      libffi:          3.4.2-h3422bc3_5          conda-forge
+      libsqlite:       3.46.0-hfb93653_0         conda-forge
+      libzlib:         1.3.1-hfb2fe0b_1          conda-forge
+      ncurses:         6.5-h7bae524_1            conda-forge
+      openssl:         3.3.1-h8359307_3          conda-forge
+      python:          3.12.5-h30c5eda_0_cpython conda-forge
+      python_abi:      3.12-5_cp312              conda-forge
+      readline:        8.2-h92ec313_1            conda-forge
+      tk:              8.6.13-h5083fa2_1         conda-forge
+      tzdata:          2024a-h8827d51_1          conda-forge
+      xz:              5.2.6-h57fd34a_0          conda-forge
+
+  Preparing transaction: ...working... done
+  Verifying transaction: ...working... done
+  Executing transaction: ...working... done
+   grep Assembly
+   flye -h
+   python -c 'import flye.tests.test_toy as t; t.main()'
+  Traceback (most recent call last):
+    File "<string>", line 1, in <module>
+    File "/opt/mambaforge/envs/bioconda/conda-bld/flye_1724856988454/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib/python3.12/site-packages/flye/tests/test_toy.py", line 18, in <module>
+      from distutils.spawn import find_executable
+  ModuleNotFoundError: No module named 'distutils'
+  WARNING: Tests failed for flye-2.9.5-py312h321ceac_0.tar.bz2 - moving package to /opt/mambaforge/envs/bioconda/conda-bld/broken
+  export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/flye_1724856988454/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac
+  export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/flye_1724856988454/test_tmp
+  Assembly of long reads with repeat graphs
+  TESTS FAILED: flye-2.9.5-py312h321ceac_0.tar.bz2
+# Last 100 lines of the build log.