Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

metasnv: add linux-aarch64 build #48913

Merged
merged 2 commits into from
Jul 4, 2024
Merged

Conversation

martin-g
Copy link
Contributor

@martin-g martin-g commented Jul 3, 2024

Describe your pull request here


Please read the guidelines for Bioconda recipes before opening a pull request (PR).

General instructions

  • If this PR adds or updates a recipe, use "Add" or "Update" appropriately as the first word in its title.
  • New recipes not directly relevant to the biological sciences need to be submitted to the conda-forge channel instead of Bioconda.
  • PRs require reviews prior to being merged. Once your PR is passing tests and ready to be merged, please issue the @BiocondaBot please add label command.
  • Please post questions on Gitter or ping @bioconda/core in a comment.

Instructions for avoiding API, ABI, and CLI breakage issues

Conda is able to record and lock (a.k.a. pin) dependency versions used at build time of other recipes.
This way, one can avoid that expectations of a downstream recipe with regards to API, ABI, or CLI are violated by later changes in the recipe.
If not already present in the meta.yaml, make sure to specify run_exports (see here for the rationale and comprehensive explanation).
Add a run_exports section like this:

build:
  run_exports:
    - ...

with ... being one of:

Case run_exports statement
semantic versioning {{ pin_subpackage("myrecipe", max_pin="x") }}
semantic versioning (0.x.x) {{ pin_subpackage("myrecipe", max_pin="x.x") }}
known breakage in minor versions {{ pin_subpackage("myrecipe", max_pin="x.x") }} (in such a case, please add a note that shortly mentions your evidence for that)
known breakage in patch versions {{ pin_subpackage("myrecipe", max_pin="x.x.x") }} (in such a case, please add a note that shortly mentions your evidence for that)
calendar versioning {{ pin_subpackage("myrecipe", max_pin=None) }}

while replacing "myrecipe" with either name if a name|lower variable is defined in your recipe or with the lowercase name of the package in quotes.

Bot commands for PR management

Please use the following BiocondaBot commands:

Everyone has access to the following BiocondaBot commands, which can be given in a comment:

@BiocondaBot please update Merge the master branch into a PR.
@BiocondaBot please add label Add the please review & merge label.
@BiocondaBot please fetch artifacts Post links to CI-built packages/containers.
You can use this to test packages locally.

Note that the @BiocondaBot please merge command is now depreciated. Please just squash and merge instead.

Also, the bot watches for comments from non-members that include @bioconda/<team> and will automatically re-post them to notify the addressed <team>.

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>
@martin-g martin-g added the aarch64 Related to adding linux-aarch64 support label Jul 3, 2024
Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>
@martin-g
Copy link
Contributor Author

martin-g commented Jul 3, 2024

@BiocondaBot please fetch artifacts

@BiocondaBot
Copy link
Collaborator

Package(s) built are ready for inspection:

Arch Package Zip File / Repodata CI Instructions
linux-64 metasnv-2.0.4-py310h0f1bec2_8.tar.bz2 LinuxArtifacts.zip Azure
showYou may also use conda to install after downloading and extracting the zip file. From the LinuxArtifacts directory: conda install -c ./packages <package name>
linux-64 metasnv-2.0.4-py311h312114e_8.tar.bz2 LinuxArtifacts.zip Azure
showYou may also use conda to install after downloading and extracting the zip file. From the LinuxArtifacts directory: conda install -c ./packages <package name>
linux-64 metasnv-2.0.4-py312hf0ab922_8.tar.bz2 LinuxArtifacts.zip Azure
showYou may also use conda to install after downloading and extracting the zip file. From the LinuxArtifacts directory: conda install -c ./packages <package name>
linux-64 metasnv-2.0.4-py38h737be40_8.tar.bz2 LinuxArtifacts.zip Azure
showYou may also use conda to install after downloading and extracting the zip file. From the LinuxArtifacts directory: conda install -c ./packages <package name>
linux-64 metasnv-2.0.4-py39had678e3_8.tar.bz2 LinuxArtifacts.zip Azure
showYou may also use conda to install after downloading and extracting the zip file. From the LinuxArtifacts directory: conda install -c ./packages <package name>
linux-aarch64 metasnv-2.0.4-py310hed11489_8.tar.bz2 repodata.json CircleCI
showYou may also use conda to install:conda install -c https://output.circle-artifacts.com/output/job/6715c48a-e4a3-4716-8a51-3848b420557f/artifacts/0/tmp/artifacts/packages <package name>
linux-aarch64 metasnv-2.0.4-py311h1560512_8.tar.bz2 repodata.json CircleCI
showYou may also use conda to install:conda install -c https://output.circle-artifacts.com/output/job/6715c48a-e4a3-4716-8a51-3848b420557f/artifacts/0/tmp/artifacts/packages <package name>
linux-aarch64 metasnv-2.0.4-py312h2c3e628_8.tar.bz2 repodata.json CircleCI
showYou may also use conda to install:conda install -c https://output.circle-artifacts.com/output/job/6715c48a-e4a3-4716-8a51-3848b420557f/artifacts/0/tmp/artifacts/packages <package name>
linux-aarch64 metasnv-2.0.4-py38hd1f0b37_8.tar.bz2 repodata.json CircleCI
showYou may also use conda to install:conda install -c https://output.circle-artifacts.com/output/job/6715c48a-e4a3-4716-8a51-3848b420557f/artifacts/0/tmp/artifacts/packages <package name>
linux-aarch64 metasnv-2.0.4-py39he43c476_8.tar.bz2 repodata.json CircleCI
showYou may also use conda to install:conda install -c https://output.circle-artifacts.com/output/job/6715c48a-e4a3-4716-8a51-3848b420557f/artifacts/0/tmp/artifacts/packages <package name>

Docker image(s) built:

Package Tag CI Install with docker
metasnv 2.0.4--py310h0f1bec2_8 Azure
showImages for Azure are in the LinuxArtifacts zip file above.gzip -dc LinuxArtifacts/images/metasnv:2.0.4--py310h0f1bec2_8.tar.gz | docker load
metasnv 2.0.4--py311h312114e_8 Azure
showImages for Azure are in the LinuxArtifacts zip file above.gzip -dc LinuxArtifacts/images/metasnv:2.0.4--py311h312114e_8.tar.gz | docker load
metasnv 2.0.4--py312hf0ab922_8 Azure
showImages for Azure are in the LinuxArtifacts zip file above.gzip -dc LinuxArtifacts/images/metasnv:2.0.4--py312hf0ab922_8.tar.gz | docker load
metasnv 2.0.4--py38h737be40_8 Azure
showImages for Azure are in the LinuxArtifacts zip file above.gzip -dc LinuxArtifacts/images/metasnv:2.0.4--py38h737be40_8.tar.gz | docker load
metasnv 2.0.4--py39had678e3_8 Azure
showImages for Azure are in the LinuxArtifacts zip file above.gzip -dc LinuxArtifacts/images/metasnv:2.0.4--py39had678e3_8.tar.gz | docker load

@martin-g
Copy link
Contributor Author

martin-g commented Jul 3, 2024

mgrigorov in 🌐 euler-arm-22 in /tmp/metasnv via 🅒 test123 took 7s 
❯ tar xvf metasnv-2.0.4-py310hed11489_8.tar.bz2                                                                                                                                                            (test123) 
info/run_exports.json
info/test/run_test.sh
info/hash_input.json
info/has_prefix
info/licenses/LICENSE
info/index.json
info/recipe/build.sh
info/recipe/meta.yaml.template
info/files
info/recipe/meta.yaml
info/recipe/conda_build_config.yaml
info/about.json
info/paths.json
info/git
bin/metaSNV_subpopr.R
share/metasnv-2.0.4/src/subpopr/R/rmNAsfromDistMatrix.R
share/metasnv-2.0.4/src/subpopr/R/filterSNVpositions.R
share/metasnv-2.0.4/src/subpopr/R/varExplainedByClusters.R
share/metasnv-2.0.4/src/subpopr/R/getSpeciesTaxonomy.R
share/metasnv-2.0.4/src/subpopr/R/collectSubpopAbunds.R
share/metasnv-2.0.4/src/subpopr/R/sampleDistCorrWithCOG.R
share/metasnv-2.0.4/src/subpopr/R/utils.R
share/metasnv-2.0.4/src/subpopr/R/importSNVresults.R
share/metasnv-2.0.4/src/subpopr/R/parseMotu2Profile.R
share/metasnv-2.0.4/src/subpopr/R/runPyScripts.R
share/metasnv-2.0.4/src/subpopr/R/psClusterStats.R
share/metasnv-2.0.4/src/subpopr/R/computeSnvFreqStats.R
share/metasnv-2.0.4/src/subpopr/R/installOrLoadPackages.R
share/metasnv-2.0.4/src/subpopr/R/assessSubpopCompleteness.R
share/metasnv-2.0.4/src/subpopr/R/filterSamples.R
share/metasnv-2.0.4/src/subpopr/R/testPredStrengthMethods.R
share/metasnv-2.0.4/src/profileSamplesUsingGenotypes.R
share/metasnv-2.0.4/src/computeDistances.R
share/metasnv-2.0.4/src/subpopr/R/snvFreqPlot.R
share/metasnv-2.0.4/src/subpopr/R/renderReports.R
share/metasnv-2.0.4/src/subpopr/R/writeSubpopAbund.R
share/metasnv-2.0.4/src/subpopr/R/writeSubpopsForAllSamples.R
share/metasnv-2.0.4/src/subpopr/R/summariseClusteringResults.R
share/metasnv-2.0.4/src/subpopr/R/clusteringStability.R
share/metasnv-2.0.4/src/subpopr/R/correlateSubpopProfileWithGeneProfiles.R
share/metasnv-2.0.4/src/subpopr/R/profileSubpops.R
share/metasnv-2.0.4/src/subpopr/R/writeGenotypeFreqs.R
share/metasnv-2.0.4/src/subpopr/R/clustering.R
share/metasnv-2.0.4/metaSNV_subpopr.R
share/metasnv-2.0.4/src/subpopr/inst/rmd/geneContentReport.rmd
share/metasnv-2.0.4/src/subpopr/inst/rmd/detailedSpeciesReport.rmd
share/metasnv-2.0.4/src/snpCaller/snpCall.o
share/metasnv-2.0.4/src/qaTools/qaCompute.o
share/metasnv-2.0.4/src/subpopr/data/TAXA.NCBI.MOTU.MAP.Rds
share/metasnv-2.0.4/src/snpCaller/.gitignore
share/metasnv-2.0.4/src/snpCaller/Makefile
share/metasnv-2.0.4/src/snpCaller/README
share/metasnv-2.0.4/src/snpCaller/snpCall
share/metasnv-2.0.4/src/qaTools/.gitignore
share/metasnv-2.0.4/src/qaTools/Makefile
share/metasnv-2.0.4/src/qaTools/qaCompute
share/metasnv-2.0.4/src/snpCaller/call_vC.cpp
share/metasnv-2.0.4/src/qaTools/qaCompute.cpp
share/metasnv-2.0.4/src/qaTools/radix.h
share/metasnv-2.0.4/src/snpCaller/gene.h
share/metasnv-2.0.4/src/subpopr/inst/rmd/resultsSummary.Rmd
bin/metaSNV.py
bin/metaSNV_DistDiv.py
bin/metaSNV_Filtering.py
share/metasnv-2.0.4/src/subpopr/inst/convertSNVtoAlleleFreq.py
share/metasnv-2.0.4/src/collapse_coverages.py
share/metasnv-2.0.4/src/createOptimumSplit.py
share/metasnv-2.0.4/src/computeGenomeCoverage.py
share/metasnv-2.0.4/src/subpopr/inst/getGenotypingSNVSubset.py
share/metasnv-2.0.4/src/gff2metaSNV_annotation.py
share/metasnv-2.0.4/metaSNV.py
share/metasnv-2.0.4/metaSNV_Filtering.py
share/metasnv-2.0.4/metaSNV_DistDiv.py
share/metasnv-2.0.4/src/subpopr/inst/__pycache__/convertSNVtoAlleleFreq.cpython-310.pyc
share/metasnv-2.0.4/src/__pycache__/computeGenomeCoverage.cpython-310.pyc
share/metasnv-2.0.4/src/subpopr/inst/__pycache__/getGenotypingSNVSubset.cpython-310.pyc
share/metasnv-2.0.4/src/__pycache__/createOptimumSplit.cpython-310.pyc
share/metasnv-2.0.4/src/__pycache__/collapse_coverages.cpython-310.pyc
share/metasnv-2.0.4/src/__pycache__/gff2metaSNV_annotation.cpython-310.pyc
share/metasnv-2.0.4/__pycache__/metaSNV_Filtering.cpython-310.pyc
share/metasnv-2.0.4/__pycache__/metaSNV.cpython-310.pyc
share/metasnv-2.0.4/__pycache__/metaSNV_DistDiv.cpython-310.pyc

mgrigorov in 🌐 euler-arm-22 in /tmp/metasnv via 🅒 test123 
❯ file bin/*                                                                                                                                                                                               (test123) 
bin/metaSNV.py:           Bourne-Again shell script, ASCII text executable
bin/metaSNV_DistDiv.py:   Bourne-Again shell script, ASCII text executable
bin/metaSNV_Filtering.py: Bourne-Again shell script, ASCII text executable
bin/metaSNV_subpopr.R:    Bourne-Again shell script, ASCII text executable


mgrigorov in 🌐 euler-arm-22 in /tmp/metasnv via 🅒 test123 
❯ file share/metasnv-2.0.4/src/snpCaller/snpCall.o                                                                                                                                                         (test123) 
share/metasnv-2.0.4/src/snpCaller/snpCall.o: ELF 64-bit LSB relocatable, ARM aarch64, version 1 (GNU/Linux), not stripped

mgrigorov in 🌐 euler-arm-22 in /tmp/metasnv via 🅒 test123 
❯ file share/metasnv-2.0.4/src/qaTools/qaCompute.o                                                                                                                                                         (test123) 
share/metasnv-2.0.4/src/qaTools/qaCompute.o: ELF 64-bit LSB relocatable, ARM aarch64, version 1 (GNU/Linux), not stripped

LGTM!

@martin-g
Copy link
Contributor Author

martin-g commented Jul 3, 2024

@BiocondaBot please add label

@BiocondaBot BiocondaBot added the please review & merge set to ask for merge label Jul 3, 2024
@bgruening bgruening merged commit 3e69ee8 into bioconda:master Jul 4, 2024
6 checks passed
@martin-g martin-g deleted the aarch64-metasnv branch July 4, 2024 09:09
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
aarch64 Related to adding linux-aarch64 support please review & merge set to ask for merge
Projects
None yet
Development

Successfully merging this pull request may close these issues.

None yet

3 participants