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Update piscem to 0.12.0 #53439

Merged
merged 3 commits into from
Jan 24, 2025
Merged

Update piscem to 0.12.0 #53439

merged 3 commits into from
Jan 24, 2025

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Update piscem: 0.11.0 → 0.12.0

install with bioconda Conda

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Recipe recipes/piscem (click to view/edit other files)
Summary piscem is a next-generation compacted colored de Bruijn Graph-based indexer and mapper
Home https://github.com/COMBINE-lab/piscem
Releases https://github.com/COMBINE-lab/piscem/releases
Author @COMBINE-lab

This pull request was automatically generated (see docs).

@BiocondaBot BiocondaBot added autobump Automatic Version Update new version labels Jan 23, 2025
@rob-p
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rob-p commented Jan 24, 2025

Hi @bgruening (or anyone expert in this); any idea what might be going on here? I tested this locally on the failing platform (an x86-64 MacOS machine), and everything compiled fine and ran without the error we're seeing on CI. The tail of that output looks like:

01:45:13 BIOCONDA INFO (OUT) Fixing permissions
01:45:13 BIOCONDA INFO (OUT) Packaged license file/s.
01:45:13 BIOCONDA INFO (OUT) INFO :: Time taken to mark (prefix)
01:45:13 BIOCONDA INFO (OUT)         0 replacements in 0 files was 0.63 seconds
01:45:13 BIOCONDA INFO (OUT) TEST START: /Users/rob/micromamba/envs/bioconda/conda-bld/osx-64/piscem-0.12.0-h01bcbec_0.tar.bz2
01:45:13 BIOCONDA INFO (OUT) Renaming work directory '/Users/rob/micromamba/envs/bioconda/conda-bld/piscem_1737699686474/work' to '/Users/rob/micromamba/envs/bioconda/conda-bld/piscem_1737699686474/work_moved_piscem-0.12.0-h01bcbec_0_osx-64'
01:45:13 BIOCONDA INFO (OUT) shutil.move(work)=/Users/rob/micromamba/envs/bioconda/conda-bld/piscem_1737699686474/work, dest=/Users/rob/micromamba/envs/bioconda/conda-bld/piscem_1737699686474/work_moved_piscem-0.12.0-h01bcbec_0_osx-64)
.01:46:02 BIOCONDA INFO (OUT) Reloading output folder (local): ...working... done
01:46:02 BIOCONDA INFO (OUT) Solving environment (_test_env): ...working... done
01:46:03 BIOCONDA INFO (OUT)
01:46:03 BIOCONDA INFO (OUT) ## Package Plan ##
01:46:03 BIOCONDA INFO (OUT)
01:46:03 BIOCONDA INFO (OUT)   environment location: /Users/rob/micromamba/envs/bioconda/conda-bld/piscem_1737699686474/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh
01:46:03 BIOCONDA INFO (OUT)
01:46:03 BIOCONDA INFO (OUT)
01:46:03 BIOCONDA INFO (OUT) The following NEW packages will be INSTALLED:
01:46:03 BIOCONDA INFO (OUT)
01:46:03 BIOCONDA INFO (OUT)     bzip2:       1.0.8-hfdf4475_7  conda-forge
01:46:03 BIOCONDA INFO (OUT)     libcxx:      19.1.7-hf95d169_0 conda-forge
01:46:03 BIOCONDA INFO (OUT)     libjemalloc: 5.3.0-hac325c4_1  conda-forge
01:46:03 BIOCONDA INFO (OUT)     libzlib:     1.3.1-hd23fc13_2  conda-forge
01:46:03 BIOCONDA INFO (OUT)     piscem:      0.12.0-h01bcbec_0 local
01:46:03 BIOCONDA INFO (OUT)
01:46:03 BIOCONDA INFO (OUT) Preparing transaction: ...working... done
01:46:04 BIOCONDA INFO (OUT) Verifying transaction: ...working... done
01:46:04 BIOCONDA INFO (OUT) Executing transaction: ...working... done
01:46:06 BIOCONDA INFO (ERR) + piscem --help
01:46:06 BIOCONDA INFO (ERR) + exit 0
01:46:08 BIOCONDA INFO (OUT) export PREFIX=/Users/rob/micromamba/envs/bioconda/conda-bld/piscem_1737699686474/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh
01:46:08 BIOCONDA INFO (OUT) export SRC_DIR=/Users/rob/micromamba/envs/bioconda/conda-bld/piscem_1737699686474/test_tmp
01:46:08 BIOCONDA INFO (OUT) Indexing and mapping to compacted colored de Bruijn graphs
01:46:08 BIOCONDA INFO (OUT)
01:46:08 BIOCONDA INFO (OUT) Usage: piscem [OPTIONS] <COMMAND>
01:46:08 BIOCONDA INFO (OUT)
01:46:08 BIOCONDA INFO (OUT) Commands:
01:46:08 BIOCONDA INFO (OUT)   build        Index a reference sequence
01:46:08 BIOCONDA INFO (OUT)   map-sc       map reads for single-cell processing
01:46:08 BIOCONDA INFO (OUT)   map-bulk     map reads for bulk processing
01:46:08 BIOCONDA INFO (OUT)   map-sc-atac  map reads for scAtac processing
01:46:08 BIOCONDA INFO (OUT)   help         Print this message or the help of the given subcommand(s)
01:46:08 BIOCONDA INFO (OUT)
01:46:08 BIOCONDA INFO (OUT) Options:
01:46:08 BIOCONDA INFO (OUT)   -q, --quiet    be quiet (no effect yet for cDBG building phase of indexing)
01:46:08 BIOCONDA INFO (OUT)   -h, --help     Print help
01:46:08 BIOCONDA INFO (OUT)   -V, --version  Print version
01:46:08 BIOCONDA INFO (OUT)
01:46:08 BIOCONDA INFO (OUT) Resource usage statistics from testing piscem:
01:46:08 BIOCONDA INFO (OUT)    Process count: 4
01:46:08 BIOCONDA INFO (OUT)    CPU time: Sys=0:00:00.0, User=0:00:00.1
01:46:08 BIOCONDA INFO (OUT)    Memory: 10.2M
01:46:08 BIOCONDA INFO (OUT)    Disk usage: 24B
01:46:08 BIOCONDA INFO (OUT)    Time elapsed: 0:00:04.1
01:46:08 BIOCONDA INFO (OUT)
01:46:08 BIOCONDA INFO (OUT)
01:46:08 BIOCONDA INFO (OUT) TEST END: /Users/rob/micromamba/envs/bioconda/conda-bld/osx-64/piscem-0.12.0-h01bcbec_0.tar.bz2
01:46:08 BIOCONDA INFO (OUT) Renaming work directory '/Users/rob/micromamba/envs/bioconda/conda-bld/piscem_1737699686474/work' to '/Users/rob/micromamba/envs/bioconda/conda-bld/piscem_1737699686474/work_moved_piscem-0.12.0-h01bcbec_0_osx-64_main_build_loop'
01:46:08 BIOCONDA INFO (OUT) shutil.move(work)=/Users/rob/micromamba/envs/bioconda/conda-bld/piscem_1737699686474/work, dest=/Users/rob/micromamba/envs/bioconda/conda-bld/piscem_1737699686474/work_moved_piscem-0.12.0-h01bcbec_0_osx-64_main_build_loop)
01:46:20 BIOCONDA INFO (OUT) # Automatic uploading is disabled
01:46:20 BIOCONDA INFO (OUT) # If you want to upload package(s) to anaconda.org later, type:
01:46:20 BIOCONDA INFO (OUT)
01:46:20 BIOCONDA INFO (OUT)
01:46:20 BIOCONDA INFO (OUT) # To have conda build upload to anaconda.org automatically, use
01:46:20 BIOCONDA INFO (OUT) # conda config --set anaconda_upload yes
01:46:20 BIOCONDA INFO (OUT) anaconda upload \
01:46:20 BIOCONDA INFO (OUT)     /Users/rob/micromamba/envs/bioconda/conda-bld/osx-64/piscem-0.12.0-h01bcbec_0.tar.bz2
01:46:20 BIOCONDA INFO (OUT) anaconda_upload is not set.  Not uploading wheels: []
01:46:20 BIOCONDA INFO (OUT)
01:46:20 BIOCONDA INFO (OUT) INFO :: The inputs making up the hashes for the built packages are as follows:
01:46:20 BIOCONDA INFO (OUT) {
01:46:20 BIOCONDA INFO (OUT)   "piscem-0.12.0-h01bcbec_0.tar.bz2": {
01:46:20 BIOCONDA INFO (OUT)     "recipe": {
01:46:20 BIOCONDA INFO (OUT)       "CONDA_BUILD_SYSROOT": "",
01:46:20 BIOCONDA INFO (OUT)       "__osx": "__osx >=10.13",
01:46:20 BIOCONDA INFO (OUT)       "bzip2": "1",
01:46:20 BIOCONDA INFO (OUT)       "channel_targets": "bioconda main",
01:46:20 BIOCONDA INFO (OUT)       "cxx_compiler": "clangxx",
01:46:20 BIOCONDA INFO (OUT)       "cxx_compiler_version": "18",
01:46:20 BIOCONDA INFO (OUT)       "rust_compiler": "rust",
01:46:20 BIOCONDA INFO (OUT)       "target_platform": "osx-64",
01:46:20 BIOCONDA INFO (OUT)       "zlib": "1"
01:46:20 BIOCONDA INFO (OUT)     }
01:46:20 BIOCONDA INFO (OUT)   }
01:46:20 BIOCONDA INFO (OUT) }
01:46:20 BIOCONDA INFO (OUT)
01:46:20 BIOCONDA INFO (OUT)
01:46:20 BIOCONDA INFO (OUT) ####################################################################################
01:46:20 BIOCONDA INFO (OUT) Resource usage summary:
01:46:20 BIOCONDA INFO (OUT)
01:46:20 BIOCONDA INFO (OUT) Total time: 0:24:54.2
01:46:20 BIOCONDA INFO (OUT) CPU usage: sys=0:00:28.5, user=0:14:21.7
01:46:20 BIOCONDA INFO (OUT) Maximum memory usage observed: 1.2G
01:46:20 BIOCONDA INFO (OUT) Total disk usage observed (not including envs): 1.3M
.
01:46:30 BIOCONDA INFO BUILD SUCCESS piscem-0.12.0-h01bcbec_0.tar.bz2
01:46:30 BIOCONDA INFO Finished build for recipes/piscem Free disk space: 37684.91 MB. Free memory: 8393.80 MB (51.23%)
01:46:30 BIOCONDA INFO (COMMAND) conda build purge
01:46:31 BIOCONDA INFO BUILD SUMMARY: successfully built 1 of 1 recipes

@martin-g
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Reason: tried: '/opt/mambaforge/envs/bioconda/pkgs/ld64_osx-64-951.9-hc8d1a19_2/bin/../lib/libtapi.dylib' (no such file),

Do you need to add tapi to the host requirements ?!

@rob-p
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rob-p commented Jan 24, 2025

I've never even heard of libtapi until now ;P! Anyway, I added it as an [osx and x86-64] dependency to host. Let's see if that works.

rob-p
rob-p approved these changes Jan 24, 2025
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After some work on macOS, x86-64, it looks good!

@rob-p rob-p merged commit f82f0cc into master Jan 24, 2025
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@rob-p rob-p deleted the bump/piscem branch January 24, 2025 14:50
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rob-p commented Jan 24, 2025

Thanks @martin-g! It worked. This is, as I said, the first I’ve ever heard of libtapi so thanks for suggesting this; it would have taken me a long time to stumble on that.

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