gsalign: add linux-aarch64 build

[martin-g]

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[martin-g]

Depends on:

• https://github.com/hsinnan75/GSAlign/pull/24

[martin-g]

The Mac OSX build fails due to:

 (ERR) dyld[17579]: Library not loaded: '@rpath/libclang-cpp.15.dylib'[0m
2024-04-24T14:37:25.4894410Z 14:37:19 [32mBIOCONDA INFO[0m (ERR)   Referenced from: '/opt/mambaforge/envs/bioconda/pkgs/clang-15-15.0.7-default_h7151d67_5/bin/clang-15'[0m
2024-04-24T14:37:25.4896810Z 14:37:19 [32mBIOCONDA INFO[0m (ERR)   Reason: tried: '/opt/mambaforge/envs/bioconda/pkgs/clang-15-15.0.7-default_h7151d67_5/bin/../lib/libclang-cpp.15.dylib' (no such file), '/opt/mambaforge/envs/bioconda/pkgs/clang-15-15.0.7-default_h7151d67_5/bin/../lib/libclang-cpp.15.dylib' (no such file), '/opt/mambaforge/envs/bioconda/pkgs/clang-15-15.0.7-default_h7151d67_5/bin/../lib/libclang-cpp.15.dylib' (no such file), '/opt/mambaforge/envs/bioconda/pkgs/clang-15-15.0.7-default_h7151d67_5/bin/../lib/libclang-cpp.15.dylib' (no such file), '/usr/local/lib/libclang-cpp.15.dylib' (no such file), '/usr/lib/libclang-cpp.15.dylib' (no such file)[0m
2024-04-24T14:37:25.4898590Z 14:37:19 [32mBIOCONDA INFO[0m (ERR) dyld[17580]: Library not loaded: '@rpath/libclang-cpp.15.dylib'[0m
2024-04-24T14:37:25.4899160Z 14:37:19 [32mBIOCONDA INFO[0m (ERR)   Referenced from: '/opt/mambaforge/envs/bioconda/pkgs/clang-15-15.0.7-default_h7151d67_5/bin/clang-15'[0m
2024-04-24T14:37:33.1340360Z 14:37:19 [32mBIOCONDA INFO[0m (ERR)   Reason: tried: '/opt/mambaforge/envs/bioconda/pkgs/clang-15-15.0.7-default_h7151d67_5/bin/../lib/libclang-cpp.15.dylib' (no such file), '/opt/mambaforge/envs/bioconda/pkgs/clang-15-15.0.7-default_h7151d67_5/bin/../lib/libclang-cpp.15.dylib' (no such file), '/opt/mambaforge/envs/bioconda/pkgs/clang-15-15.0.7-default_h7151d67_5/bin/../lib/libclang-cpp.15.dylib' (no such file), '/opt/mambaforge/envs/bioconda/pkgs/clang-15-15.0.7-default_h7151d67_5/bin/../lib/libclang-cpp.15.dylib' (no such file), '/usr/local/lib/libclang-cpp.15.dylib' (no such file), '/usr/lib/libclang-cpp.15.dylib' (no such file)[0m
2024-04-24T14:37:33.1343110Z 14:37:19 [32mBIOCONDA INFO[0m (ERR) make: *** [makefile:9: bwt.o] Abort trap: 6[0m
2024-04-24T14:37:33.1343540Z 14:37:19 [32mBIOCONDA INFO[0m (ERR) make: *** Waiting for unfinished jobs....[0m
2024-04-24T14:37:33.1344110Z 14:37:19 [32mBIOCONDA INFO[0m (ERR) make: *** [makefile:9: utils.o] Abort trap: 6[0m

Any ideas ?

[martin-g]

@BiocondaBot please fetch artifacts

[BiocondaBot]

Package(s) built are ready for inspection:

Arch	Package	Zip File / Repodata	CI	Instructions
linux-64	gsalign-1.0.22-h8b853e6_5.tar.bz2	LinuxArtifacts.zip	Azure	show You 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	gsalign-1.0.22-h7f8aa1e_5.tar.bz2	repodata.json	CircleCI	show You may also use conda to install:conda install -c https://output.circle-artifacts.com/output/job/a015c32b-9760-4e6d-bd83-54616d9383f6/artifacts/0/tmp/artifacts/packages <package name>

---

Docker image(s) built:

Package	Tag	CI	Install with docker
gsalign	1.0.22--h8b853e6_5	Azure	show Images for Azure are in the LinuxArtifacts zip file above.gzip -dc LinuxArtifacts/images/gsalign:1.0.22--h8b853e6_5.tar.gz | docker load

[martin-g]

The Linux ARM64 artifacts look good:

mgrigorov in 🌐 euler-arm-22 in /tmp/gsalign via 🅒 test123 took 4s 
❯ tar jxvf gsalign-1.0.22-h7f8aa1e_5.tar.bz2                                                                                                                                                               (test123) 
info/files
info/run_exports.json
info/test/run_test.sh
info/hash_input.json
info/index.json
info/paths.json
info/recipe/build.sh
info/recipe/meta.yaml.template
info/licenses/LICENSE
info/recipe/meta.yaml
info/recipe/conda_build_config.yaml
info/about.json
info/git
info/recipe/support-linux-aarch64.patch
bin/bwt_index
bin/GSAlign

mgrigorov in 🌐 euler-arm-22 in /tmp/gsalign via 🅒 test123 
❯ file ./bin/*                                                                                                                                                                                             (test123) 
./bin/bwt_index: ELF 64-bit LSB pie executable, ARM aarch64, version 1 (SYSV), dynamically linked, interpreter /lib/ld-linux-aarch64.so.1, for GNU/Linux 3.7.0, not stripped
./bin/GSAlign:   ELF 64-bit LSB pie executable, ARM aarch64, version 1 (SYSV), dynamically linked, interpreter /lib/ld-linux-aarch64.so.1, for GNU/Linux 3.7.0, not stripped

mgrigorov in 🌐 euler-arm-22 in /tmp/gsalign via 🅒 test123 
❯ ./bin/GSAlign                                                                                                                                                                                            (test123) 

GenAlign v1.0.22
Usage: ./bin/GSAlign [-i IndexFile Prefix / -r Reference file] -q QueryFile[Fasta]

Options: -t     INT     number of threads [8]
         -o     STR     Set the prefix of the output files [output]
         -fmt   INT     Set the output format 1:maf, 2:aln [1]
         -idy   INT     Set the minimal sequence identity (0-100) of a local alignment [70]
         -slen  INT     Set the minimal seed length [15]
         -alen  INT     Set the minimal alignment length [200]
         -ind   INT     Set the maximal indel size [25]
         -clr   INT     Set the minimal cluster size [200]
         -unique        Output unique alignment only [false]
         -sen           Sensitive mode [False]
         -dp            Output Dot-plots
         -one           set one on one aligment mode[false]
         -gp    STR     Specify the path of gnuplot

[martin-g]

@BiocondaBot please add label