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scalpel: add linux-aarch64 build #47964

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merged 3 commits into from
May 23, 2024
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Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
@martin-g martin-g added the aarch64 Related to adding linux-aarch64 support label May 21, 2024
Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
…for Linux ARM64

Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
martin-g added a commit to martin-g/bioconda-utils that referenced this pull request May 21, 2024
2.5.2 is the only version at the moment that provides linux-aarch64
package: https://anaconda.org/bioconda/bamtools/files

I faced the following error
```
WARNING: failed to get package records, retrying.  exception was: Unsatisfiable dependencies for platform linux-aarch64: {MatchSpec("bamtools=2.5.1")}
Encountered problems while solving:
  - nothing provides requested bamtools 2.5.1.*
```
while adding linux-aarch64 to `scalpel`
  (bioconda/bioconda-recipes#47964)

Full logs with the error:
- https://circleci.com/api/v1.1/project/github/bioconda/bioconda-recipes/186948/output/107/0?file=true&allocation-id=664c88870a2ca54ac5eb924f-0-build%2FABCDEFGH

Successful build after adding custom conda_build_config.yaml for
scalpel:
- https://app.circleci.com/pipelines/github/bioconda/bioconda-recipes/116194/workflows/00d6dc8f-1d05-48a5-b15f-1ae3bff71433/jobs/186951

Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
@martin-g
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martin-g commented May 21, 2024

The Linux ARM64 build fails with:

WARNING: failed to get package records, retrying.  exception was: Unsatisfiable dependencies for platform linux-aarch64: {MatchSpec("bamtools=2.5.1")}
Encountered problems while solving:
  - nothing provides requested bamtools 2.5.1.*

I think it is caused by https://github.com/bioconda/bioconda-utils/blob/09d108e796cb4fce317c475b7d26bbaea124619c/bioconda_utils/bioconda_utils-conda_build_config.yaml#L26

Update: I've created bioconda/bioconda-utils#988 for this issue!

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@BiocondaBot please fetch artifacts

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Package(s) built are ready for inspection:

Arch Package Zip File / Repodata CI Instructions
linux-64 scalpel-0.5.4-h2df6261_6.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 scalpel-0.5.4-h8e97bb7_6.tar.bz2 repodata.json CircleCI
showYou may also use conda to install:conda install -c https://output.circle-artifacts.com/output/job/15e29f08-d94b-47bc-a1f7-6cfdb75d346c/artifacts/0/tmp/artifacts/packages <package name>

Docker image(s) built:

Package Tag CI Install with docker
scalpel 0.5.4--h2df6261_6 Azure
showImages for Azure are in the LinuxArtifacts zip file above.gzip -dc LinuxArtifacts/images/scalpel:0.5.4--h2df6261_6.tar.gz | docker load

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mgrigorov in 🌐 euler-arm-22 in /tmp/scalpel via 🅒 test123 took 11s 
❯ tar xvf scalpel-0.5.4-h8e97bb7_6.tar.bz2                                                                                                                                                                 (test123) 
info/run_exports.json
info/test/run_test.sh
info/hash_input.json
info/has_prefix
info/index.json
info/recipe/meta.yaml.template
info/recipe/build.sh
info/recipe/meta.yaml
info/recipe/conda_build_config.yaml
info/about.json
info/files
info/git
info/paths.json
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share/scalpel-0.5.4-6/samtools-1.1/misc/blast2sam.pl
share/scalpel-0.5.4-6/samtools-1.1/misc/interpolate_sam.pl
share/scalpel-0.5.4-6/samtools-1.1/htslib-1.1/test/test.pl
share/scalpel-0.5.4-6/bcftools-1.1/htslib-1.1/test/test.pl
share/scalpel-0.5.4-6/samtools-1.1/misc/novo2sam.pl
share/scalpel-0.5.4-6/samtools-1.1/misc/sam2vcf.pl
share/scalpel-0.5.4-6/samtools-1.1/misc/seq_cache_populate.pl
share/scalpel-0.5.4-6/samtools-1.1/misc/samtools.pl
share/scalpel-0.5.4-6/samtools-1.1/misc/export2sam.pl
share/scalpel-0.5.4-6/bcftools-1.1/vcfutils.pl
share/scalpel-0.5.4-6/FindSomatic.pl
share/scalpel-0.5.4-6/FindDenovos.pl
share/scalpel-0.5.4-6/FindVariants.pl
share/scalpel-0.5.4-6/bcftools-1.1/test/test.pl
share/scalpel-0.5.4-6/samtools-1.1/test/test.pl

mgrigorov in 🌐 euler-arm-22 in /tmp/scalpel via 🅒 test123 
❯ ll                                                                                                                                                                                                       (test123) 
total 9.6M
drwxr-xr-x 2 mgrigorov mgrigorov   80 May 23 12:08 bin
drwxr-xr-x 4 mgrigorov mgrigorov  240 May 23 12:08 info
-rw-r--r-- 1 mgrigorov mgrigorov 9.6M May 21 12:20 scalpel-0.5.4-h8e97bb7_6.tar.bz2
drwxr-xr-x 3 mgrigorov mgrigorov   60 May 23 12:08 share

mgrigorov in 🌐 euler-arm-22 in /tmp/scalpel via 🅒 test123 
❯ file bin/*                                                                                                                                                                                               (test123) 
bin/scalpel-discovery: symbolic link to ../share/scalpel-0.5.4-6/scalpel-discovery
bin/scalpel-export:    symbolic link to ../share/scalpel-0.5.4-6/scalpel-export

mgrigorov in 🌐 euler-arm-22 in /tmp/scalpel via 🅒 test123 
❯ ./bin/scalpel-discovery                                                                                                                                                                                  (test123) 
Local date and time: Thu May 23 12:08:37 2024

Program: scalpel-discovery (micro-assembly variant detection)
Version: 0.5.4 (beta), January 11 2018
Contact: Giuseppe Narzisi <gnarzisi@nygenome.org>

usage: scalpel-discovery <COMMAND> [OPTIONS]

COMMAND:

    --help    : this (help) message
    --verbose : verbose mode

    --single  : single exome study 
    --denovo  : family study (mom,dad,affected,sibling)
    --somatic : normal/tumor study

LGTM!

@martin-g
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@BiocondaBot please add label

@BiocondaBot BiocondaBot added the please review & merge set to ask for merge label May 23, 2024
@mencian mencian merged commit 00c8ea2 into bioconda:master May 23, 2024
6 checks passed
@martin-g martin-g deleted the aarch64-scalpel branch May 27, 2024 07:13
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