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cgat-apps: add aarch64/arm64 builds #52519

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merged 4 commits into from
Dec 6, 2024

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@martin-g martin-g commented Dec 2, 2024

Describe your pull request here


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Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>
@martin-g martin-g added aarch64 Related to adding linux-aarch64 support osx-arm64 Related to adding osx-arm64 support labels Dec 2, 2024
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martin-g commented Dec 5, 2024

The OSX ARM64 build fails with:

14:53:38 BIOCONDA INFO (ERR) The following packages are incompatible
14:53:38 BIOCONDA INFO (ERR) ├─ numpy >=1.23.5,<2.0a0  is requested and can be installed;
14:53:38 BIOCONDA INFO (ERR) └─ pybigwig is not installable because there are no viable options
14:53:38 BIOCONDA INFO (ERR)    ├─ pybigwig 0.3.23 would require
14:53:38 BIOCONDA INFO (ERR)    │  └─ numpy >=2.1.3,<3.0a0  but there are no viable options
14:53:38 BIOCONDA INFO (ERR)    │     ├─ numpy [2.1.0rc1|2.2.0rc1] would require
14:53:38 BIOCONDA INFO (ERR)    │     │  └─ _numpy_rc, which does not exist (perhaps a missing channel);
14:53:38 BIOCONDA INFO (ERR)    │     └─ numpy 2.1.3 conflicts with any installable versions previously reported;
14:53:38 BIOCONDA INFO (ERR)    └─ pybigwig 0.3.23 would require
14:53:38 BIOCONDA INFO (ERR)       └─ numpy >=2.0.2,<3.0a0  but there are no viable options
14:53:38 BIOCONDA INFO (ERR)          ├─ numpy [2.0.2|2.1.0|2.1.1|2.1.2] conflicts with any installable versions previously reported;
14:53:38 BIOCONDA INFO (ERR)          ├─ numpy [2.1.0rc1|2.2.0rc1], which cannot be installed (as previously explained);
14:53:38 BIOCONDA INFO (ERR)          └─ numpy 2.1.3 conflicts with any installable versions previously reported.

recipes/cgat-apps/meta.yaml Outdated Show resolved Hide resolved
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martin-g commented Dec 6, 2024

@BiocondaBot please fetch artifacts

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Package(s) built are ready for inspection:

Arch Package Zip File / Repodata CI Instructions
linux-64 cgat-apps-0.7.10-py310hc1935f2_1.tar.bz2 linux-64.zip GitHub Actions
showYou may also use conda to install after downloading and extracting the zip file. conda install -c ./packages <package name>
linux-64 cgat-apps-0.7.10-py311h251f972_1.tar.bz2 linux-64.zip GitHub Actions
showYou may also use conda to install after downloading and extracting the zip file. conda install -c ./packages <package name>
linux-64 cgat-apps-0.7.10-py312he77ef44_1.tar.bz2 linux-64.zip GitHub Actions
showYou may also use conda to install after downloading and extracting the zip file. conda install -c ./packages <package name>
osx-64 cgat-apps-0.7.10-py310hfad6fbf_1.tar.bz2 osx-64.zip GitHub Actions
showYou may also use conda to install after downloading and extracting the zip file. conda install -c ./packages <package name>
osx-64 cgat-apps-0.7.10-py311h282d8cc_1.tar.bz2 osx-64.zip GitHub Actions
showYou may also use conda to install after downloading and extracting the zip file. conda install -c ./packages <package name>
osx-64 cgat-apps-0.7.10-py312h4908a77_1.tar.bz2 osx-64.zip GitHub Actions
showYou may also use conda to install after downloading and extracting the zip file. conda install -c ./packages <package name>
linux-aarch64 cgat-apps-0.7.10-py310ha0bf786_1.tar.bz2 repodata.json CircleCI
showYou may also use conda to install:conda install -c https://output.circle-artifacts.com/output/job/344e00ac-ef8e-49b1-855b-9a70740be236/artifacts/0/tmp/artifacts/packages <package name>
linux-aarch64 cgat-apps-0.7.10-py311h132dfe1_1.tar.bz2 repodata.json CircleCI
showYou may also use conda to install:conda install -c https://output.circle-artifacts.com/output/job/344e00ac-ef8e-49b1-855b-9a70740be236/artifacts/0/tmp/artifacts/packages <package name>
linux-aarch64 cgat-apps-0.7.10-py312h2b6caad_1.tar.bz2 repodata.json CircleCI
showYou may also use conda to install:conda install -c https://output.circle-artifacts.com/output/job/344e00ac-ef8e-49b1-855b-9a70740be236/artifacts/0/tmp/artifacts/packages <package name>

Docker image(s) built:

Package Tag CI Install with docker
cgat-apps 0.7.10--py310hc1935f2_1 GitHub Actions
showImages are in the linux-64 zip file above.gzip -dc images/cgat-apps---0.7.10--py310hc1935f2_1.tar.gz | docker load
cgat-apps 0.7.10--py312he77ef44_1 GitHub Actions
showImages are in the linux-64 zip file above.gzip -dc images/cgat-apps---0.7.10--py312he77ef44_1.tar.gz | docker load
cgat-apps 0.7.10--py311h251f972_1 GitHub Actions
showImages are in the linux-64 zip file above.gzip -dc images/cgat-apps---0.7.10--py311h251f972_1.tar.gz | docker load

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martin-g commented Dec 6, 2024

mgrigorov in 🌐 euler-arm-22 in /tmp/cgat-apps via 🅒 test123 took 3s 
❯ tar xvf cgat-apps-0.7.10-py310ha0bf786_1.tar.bz2                                                                                                                                                         (test123) 
info/test/run_test.py
info/run_exports.json
info/test/run_test.sh
info/hash_input.json
info/has_prefix
info/recipe/build.sh
info/index.json
info/licenses/LICENSE
info/recipe/meta.yaml.template
info/recipe/meta.yaml
info/recipe/conda_build_config.yaml
info/about.json
info/files
info/paths.json
info/git
lib/python3.10/site-packages/cgat/Components/connected_components.cpp
bin/cgat
lib/python3.10/site-packages/cgat/tools/cgat_script_template.py
lib/python3.10/site-packages/cgat/Glam2.py
lib/python3.10/site-packages/cgat/tools/fastq2tsv.py
lib/python3.10/site-packages/cgat/Histogram2D.py
lib/python3.10/site-packages/cgat/tools/csv2csv.py
lib/python3.10/site-packages/cgat/Glam2Scan.py
lib/python3.10/site-packages/cgat/RLE.py
lib/python3.10/site-packages/cgat/Iterators.py
lib/python3.10/site-packages/cgat/tools/fastq2fasta.py
lib/python3.10/site-packages/cgat/tools/bam2bam_split_reads.py
lib/python3.10/site-packages/doc/collect.py
lib/python3.10/site-packages/doc/python/Trackers.py
lib/python3.10/site-packages/cgat/AString.py
lib/python3.10/site-packages/scripts/conda.py
lib/python3.10/site-packages/cgat/tools/bed2graph.py
lib/python3.10/site-packages/cgat/tools/fastas2fasta.py
lib/python3.10/site-packages/cgat/Motifs.py
lib/python3.10/site-packages/cgat/tools/table2table.py
lib/python3.10/site-packages/cgat/tools/bam2window_stats.py
lib/python3.10/site-packages/cgat/tools/fasta2vcf.py
lib/python3.10/site-packages/cgat/tools/cgat_rebuild_extensions.py
lib/python3.10/site-packages/cgat/tools/genome_bed.py
lib/python3.10/site-packages/cgat/tools/fasta2stats.py
lib/python3.10/site-packages/cgat/AGP.py
lib/python3.10/site-packages/cgat/tools/table2stats.py
lib/python3.10/site-packages/cgat/GFF3.py
lib/python3.10/site-packages/cgat/VCF.py
lib/python3.10/site-packages/cgat/tools/bcl2fastq.py
lib/python3.10/site-packages/cgat/tools/bam2depth.py
lib/python3.10/site-packages/cgat/tools/vcf_vs_vcf.py
lib/python3.10/site-packages/cgat/tools/fastqs2fastq.py
lib/python3.10/site-packages/cgat/tools/fasta2variants.py
lib/python3.10/site-packages/cgat/tools/bam_vs_bam.py
lib/python3.10/site-packages/cgat/FastaIterator.py
lib/python3.10/site-packages/cgat/tools/bed2gff.py
lib/python3.10/site-packages/cgat/tools/index2bed.py
lib/python3.10/site-packages/cgat/tools/beds2counts.py
lib/python3.10/site-packages/cgat/tools/gff2psl.py
lib/python3.10/site-packages/cgat/tools/split_gff.py
lib/python3.10/site-packages/cgat/IndexedGenome.py
lib/python3.10/site-packages/cgat/cgat.py
lib/python3.10/site-packages/cgat/tools/bed_vs_bed.py
lib/python3.10/site-packages/cgat/tools/bam2fastq.py
lib/python3.10/site-packages/cgat/tools/fastqs2fasta.py
lib/python3.10/site-packages/cgat/tools/cgat_get_options.py
lib/python3.10/site-packages/cgat/tools/fastq2summary.py
lib/python3.10/site-packages/cgat/tools/bed2stats.py
lib/python3.10/site-packages/cgat/tools/gff2bed.py
lib/python3.10/site-packages/cgat/MEME.py
lib/python3.10/site-packages/cgat/tools/fasta2kmercontent.py
lib/python3.10/site-packages/cgat/NCL/__init__.py
lib/python3.10/site-packages/cgat/RateEstimation.py
lib/python3.10/site-packages/cgat/tools/bed2fasta.py
lib/python3.10/site-packages/cgat/SetTools.py
lib/python3.10/site-packages/cgat/tools/wig2bed.py
lib/python3.10/site-packages/cgat/tools/bam2bed.py
lib/python3.10/site-packages/cgat/tools/extract_stats.py
lib/python3.10/site-packages/cgat/tools/fastq2table.py
lib/python3.10/site-packages/cgat/tools/split_fasta.py
lib/python3.10/site-packages/cgat/tools/vcfstats2db.py
lib/python3.10/site-packages/cgat/tools/vcf_stats.py
lib/python3.10/site-packages/cgat/tools/gff2stats.py
lib/python3.10/site-packages/cgat/Masker.py
lib/python3.10/site-packages/cgat/makeGeneset.py
lib/python3.10/site-packages/cgat/Sra.py
lib/python3.10/site-packages/cgat/tools/diff_bam.py
lib/python3.10/site-packages/cgat/tools/split_file.py
lib/python3.10/site-packages/cgat/tools/bam_vs_bed.py
lib/python3.10/site-packages/cgat/tools/bams2bam.py
lib/python3.10/site-packages/doc/conf.py
lib/python3.10/site-packages/cgat/tools/vcf_compare_phase.py
lib/python3.10/site-packages/cgat/tools/bam_pileup2tsv.py
lib/python3.10/site-packages/cgat/tools/bam_vs_gtf.py
lib/python3.10/site-packages/cgat/tools/data2histogram.py
lib/python3.10/site-packages/cgat/tools/fastqs2fastqs.py
lib/python3.10/site-packages/cgat/tools/diff_fasta.py
lib/python3.10/site-packages/cgat/tools/bam_compare_alignments.py
lib/python3.10/site-packages/cgat/tools/tables2table.py
lib/python3.10/site-packages/scripts/cgat_check_deps.py
lib/python3.10/site-packages/cgat/tools/gff2histogram.py
lib/python3.10/site-packages/cgat/tools/csvs2csv.py
lib/python3.10/site-packages/cgat/tools/fasta2bed.py
lib/python3.10/site-packages/cgat/tools/beds2beds.py
lib/python3.10/site-packages/cgat/tools/gff2coverage.py
lib/python3.10/site-packages/cgat/tools/vcf2tsv.py
lib/python3.10/site-packages/cgat/tools/gtfs2tsv.py
lib/python3.10/site-packages/cgat/Intervals.py
lib/python3.10/site-packages/cgat/tools/gtf2tsv.py
lib/python3.10/site-packages/cgat/tools/diff_bed.py
lib/python3.10/site-packages/cgat/tools/fastq2tpm.py
lib/python3.10/site-packages/cgat/MatrixTools.py
lib/python3.10/site-packages/cgat/tools/fasta2table.py
lib/python3.10/site-packages/cgat/tools/index_fasta.py
lib/python3.10/site-packages/cgat/tools/gff32gtf.py
lib/python3.10/site-packages/cgat/Fastq.py
lib/python3.10/site-packages/cgat/tools/gff2fasta.py
lib/python3.10/site-packages/cgat/tools/diff_gtf.py
lib/python3.10/site-packages/cgat/tools/fasta2fastq.py
lib/python3.10/site-packages/cgat/tools/vcf2vcf.py
lib/python3.10/site-packages/cgat/tools/gff2table.py
lib/python3.10/site-packages/cgat/tools/diff_chains.py
lib/python3.10/site-packages/cgat/tools/bam2fasta.py
lib/python3.10/site-packages/cgat/tools/bam2wiggle.py
lib/python3.10/site-packages/cgat/Bed.py
lib/python3.10/site-packages/cgat/tools/fastq2fastq.py
lib/python3.10/site-packages/cgat/tools/gtf2fasta.py
lib/python3.10/site-packages/cgat/Variants.py
lib/python3.10/site-packages/cgat/Histogram.py
lib/python3.10/site-packages/cgat/Tree.py
lib/python3.10/site-packages/cgat/tools/fasta2fasta.py
lib/python3.10/site-packages/cgat/tools/bed2bed.py
lib/python3.10/site-packages/cgat/tools/bed2table.py
lib/python3.10/site-packages/cgat/tools/bam2bam.py
lib/python3.10/site-packages/cgat/dictzip.py
lib/python3.10/site-packages/cgat/Blat.py
lib/python3.10/site-packages/cgat/tools/gff2gff.py
lib/python3.10/site-packages/cgat/GTF.py
lib/python3.10/site-packages/cgat/Stats.py
lib/python3.10/site-packages/cgat/tools/bam2stats.py
lib/python3.10/site-packages/cgat/tools/bam2geneprofile.py
lib/python3.10/site-packages/cgat/tools/gtf2table.py
lib/python3.10/site-packages/cgat/SequenceProperties.py
lib/python3.10/site-packages/cgat/tools/gtf2gff.py
lib/python3.10/site-packages/cgat/IndexedFasta.py
lib/python3.10/site-packages/cgat/TreeTools.py
lib/python3.10/site-packages/cgat/Genomics.py
lib/python3.10/site-packages/cgat/tools/gtf2gtf.py
lib/python3.10/site-packages/cgat/__init__.py
lib/python3.10/site-packages/cgat/tools/__init__.py
lib/python3.10/site-packages/cgat/NCL/intervaldb.c
lib/python3.10/site-packages/cgat-0.7.10.dist-info/direct_url.json
lib/python3.10/site-packages/cgat-0.7.10.dist-info/top_level.txt
lib/python3.10/site-packages/cgat-0.7.10.dist-info/entry_points.txt
lib/python3.10/site-packages/cgat/Components/connected_components.h
lib/python3.10/site-packages/cgat/NCL/default.h
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lib/python3.10/site-packages/cgat-0.7.10.dist-info/METADATA
lib/python3.10/site-packages/cgat-0.7.10.dist-info/RECORD
lib/python3.10/site-packages/cgat-0.7.10.dist-info/REQUESTED
lib/python3.10/site-packages/cgat/FastqTools/fastqtools.pyx
lib/python3.10/site-packages/cgat/Components/Components.pyx
lib/python3.10/site-packages/cgat/BamTools/peakshape.pyx
lib/python3.10/site-packages/cgat/NCL/cnestedlist.pyx
lib/python3.10/site-packages/cgat/VCFTools/vcftools.pyx
lib/python3.10/site-packages/cgat/BamTools/geneprofile.pyx
lib/python3.10/site-packages/cgat/BamTools/bamtools.pyx
lib/python3.10/site-packages/cgat/GeneModelAnalysis.pyx
lib/python3.10/site-packages/cgat/FastqTools.cpython-310-aarch64-linux-gnu.so
lib/python3.10/site-packages/cgat/Components.cpython-310-aarch64-linux-gnu.so
lib/python3.10/site-packages/cgat/BamTools/peakshape.cpython-310-aarch64-linux-gnu.so
lib/python3.10/site-packages/cgat/NCL/cnestedlist.cpython-310-aarch64-linux-gnu.so
lib/python3.10/site-packages/cgat/VCFTools.cpython-310-aarch64-linux-gnu.so
lib/python3.10/site-packages/cgat/BamTools/geneprofile.cpython-310-aarch64-linux-gnu.so
lib/python3.10/site-packages/cgat/BamTools/bamtools.cpython-310-aarch64-linux-gnu.so
lib/python3.10/site-packages/cgat/GeneModelAnalysis.cpython-310-aarch64-linux-gnu.so

mgrigorov in 🌐 euler-arm-22 in /tmp/cgat-apps via 🅒 test123 
❯ file bin/* lib/python3.10/site-packages/cgat/*.so                                                                                                                                                        (test123) 
bin/cgat:                                                                             a /opt/conda/conda-bld/cgat-apps_1733412597514/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place script, ASCII text executable
lib/python3.10/site-packages/cgat/Components.cpython-310-aarch64-linux-gnu.so:        ELF 64-bit LSB shared object, ARM aarch64, version 1 (SYSV), dynamically linked, not stripped
lib/python3.10/site-packages/cgat/FastqTools.cpython-310-aarch64-linux-gnu.so:        ELF 64-bit LSB shared object, ARM aarch64, version 1 (SYSV), dynamically linked, not stripped
lib/python3.10/site-packages/cgat/GeneModelAnalysis.cpython-310-aarch64-linux-gnu.so: ELF 64-bit LSB shared object, ARM aarch64, version 1 (SYSV), dynamically linked, not stripped
lib/python3.10/site-packages/cgat/VCFTools.cpython-310-aarch64-linux-gnu.so:          ELF 64-bit LSB shared object, ARM aarch64, version 1 (SYSV), dynamically linked, with debug_info, not stripped

LGTM!

@martin-g
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martin-g commented Dec 6, 2024

@BiocondaBot please add label

@BiocondaBot BiocondaBot added the please review & merge set to ask for merge label Dec 6, 2024
@mencian mencian merged commit f6e96ee into bioconda:master Dec 6, 2024
5 checks passed
@martin-g martin-g deleted the aarch64-cgat-apps branch December 9, 2024 12:12
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