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sortmerna: init at 3.0.3 #64669

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merged 1 commit into from Aug 27, 2019
Merged

sortmerna: init at 3.0.3 #64669

merged 1 commit into from Aug 27, 2019

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luispedro
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This is a useful package in bioinformatics, the corresponding bioconda package has > 50,000 downloads

Things done
  • Tested using sandboxing (nix.useSandbox on NixOS, or option sandbox in nix.conf on non-NixOS)
  • Built on platform(s)
    • NixOS
    • macOS
    • other Linux distributions
  • Tested execution of all binary files (usually in ./result/bin/)

@luispedro
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I had started from the bioconda package for this, but I realized that there is a newer release, but I need #64987 to be committed for the new version to compile on Nix

@worldofpeace
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@luispedro Request granted ✨

@luispedro luispedro changed the title sortmerna: init at 2.1 sortmerna: init at 3.0.3 Jul 26, 2019
@luispedro
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@worldofpeace : much appreciated. I updated the package and it compiles cleanly on top of master. Some of the previously raised issues have gone away in the new release (the headers are no longer installed by default), the remaining I fixed manually.

@luispedro
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Thanks. Forced push new version.

@luispedro luispedro force-pushed the add_sortmerna branch 3 times, most recently from c4042c3 to d2c12ee Compare August 18, 2019 15:29
@Ekleog
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Ekleog commented Aug 25, 2019

@GrahamcOfBorg build sortmerna

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Ekleog commented Aug 25, 2019

Looks like sortmerna doesn't build on aarch64-linux. Maybe either somehow fix that (not sure whether it's supposed to) or mark it as disabled by having eg. meta.platforms = "x86_64-linux"?

@luispedro
sortmerna: init at 3.0.3
bc22c2e 
This is a useful package in bioinformatics, namely in processing
short-read sequencing data from metagenomes
@luispedro
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Seeing the error and the code, it seems that it relies on using intrinsics, so it's tied to x86

@Ekleog
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Ekleog commented Aug 27, 2019

@GrahamcOfBorg build sortmerna

(checking whether it builds with x86_64-darwin, as the switch from linux to x86_64 likely enabled it)

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Ekleog commented Aug 27, 2019

Thank you!

@Ekleog Ekleog merged commit 8a4721d into NixOS:master Aug 27, 2019
@luispedro luispedro deleted the add_sortmerna branch August 28, 2019 00:25
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@tadeokondrak tadeokondrak tadeokondrak left review comments

@worldofpeace worldofpeace worldofpeace approved these changes

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8.has: package (new) 10.rebuild-darwin: 1-10 10.rebuild-linux: 1-10 11.by: package-maintainer
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@luispedro @worldofpeace @Ekleog @tadeokondrak