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sortmerna: add linux-aarch64 build and update to 4.3.7 #46644

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merged 8 commits into from
Jun 4, 2024

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@martin-g martin-g force-pushed the aarch64-ncbi-sortmerna branch 2 times, most recently from 34ef163 to dc70ac6 Compare March 21, 2024 13:34
@corneliusroemer corneliusroemer added the aarch64 Related to adding linux-aarch64 support label Mar 21, 2024
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Fix for Linux ARM64 upstream - sortmerna/sortmerna#417

@martin-g martin-g changed the title sortmerna: add linux-aarch64 build and update to 4.3.7 (beta) sortmerna: add linux-aarch64 build and update to 4.3.7 Jun 3, 2024
Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
@martin-g martin-g force-pushed the aarch64-ncbi-sortmerna branch 2 times, most recently from 4929834 to 3a15bac Compare June 4, 2024 11:31
@martin-g martin-g marked this pull request as ready for review June 4, 2024 12:21
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martin-g commented Jun 4, 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 sortmerna-4.3.7-hdbdd923_0.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 sortmerna-4.3.7-h7021222_0.tar.bz2 repodata.json CircleCI
showYou may also use conda to install:conda install -c https://output.circle-artifacts.com/output/job/f2b8433e-07ff-424f-9821-054b2daa2bfd/artifacts/0/tmp/artifacts/packages <package name>

Docker image(s) built:

Package Tag CI Install with docker
sortmerna 4.3.7--hdbdd923_0 Azure
showImages for Azure are in the LinuxArtifacts zip file above.gzip -dc LinuxArtifacts/images/sortmerna:4.3.7--hdbdd923_0.tar.gz | docker load

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martin-g commented Jun 4, 2024

mgrigorov in 🌐 euler-arm-22 in /tmp/sortmerna took 7s 
❯ tar xvf sortmerna-4.3.7-h7021222_0.tar.bz2 
info/files
info/run_exports.json
info/test/run_test.sh
info/recipe/build.sh
info/hash_input.json
info/paths.json
info/index.json
info/recipe/meta.yaml.template
info/recipe/meta.yaml
info/recipe/conda_build_config.yaml
info/licenses/LICENSE.LESSER.txt
info/about.json
info/git
bin/sortmerna

mgrigorov in 🌐 euler-arm-22 in /tmp/sortmerna 
❯ file ./bin/sortmerna 
./bin/sortmerna: ELF 64-bit LSB pie executable, ARM aarch64, version 1 (GNU/Linux), dynamically linked, interpreter /lib/ld-linux-aarch64.so.1, for GNU/Linux 3.7.0, with debug_info, not stripped

mgrigorov in 🌐 euler-arm-22 in /tmp/sortmerna 
❯ ./bin/sortmerna

[process:1388] ERROR: Missing required command options

  Program:      SortMeRNA version 4.3.7
  Copyright:    2016-2020 Clarity Genomics BVBA:
                Turnhoutseweg 30, 2340 Beerse, Belgium
                2014-2016 Knight Lab:
                Department of Pediatrics, UCSD, La Jolla
                2012-2014 Bonsai Bioinformatics Research Group:
                LIFL, University Lille 1, CNRS UMR 8022, INRIA Nord-Europe
  Disclaimer:   SortMeRNA comes with ABSOLUTELY NO WARRANTY; without even the
                implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
                See the GNU Lesser General Public License for more details.
  Contributors: Jenya Kopylova   jenya.kopylov@gmail.com
                Laurent Noé      laurent.noe@lifl.fr
                Pierre Pericard  pierre.pericard@lifl.fr
                Daniel McDonald  wasade@gmail.com
                Mikaël Salson    mikael.salson@lifl.fr
                Hélène Touzet    helene.touzet@lifl.fr
                Rob Knight       robknight@ucsd.edu

LGTM!

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martin-g commented Jun 4, 2024

@BiocondaBot please add label

@BiocondaBot BiocondaBot added the please review & merge set to ask for merge label Jun 4, 2024
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LGTM, thanks @martin-g!

@mencian mencian merged commit 997a212 into bioconda:master Jun 4, 2024
6 checks passed
@martin-g martin-g deleted the aarch64-ncbi-sortmerna branch June 5, 2024 06:59
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