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strelka: init 2.9.5 #44250

Merged
merged 1 commit into from Aug 20, 2018
Merged

strelka: init 2.9.5 #44250

merged 1 commit into from Aug 20, 2018

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jbedo
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@jbedo jbedo commented Jul 31, 2018

Motivation for this change

Strelka init at version 2.9.5.

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 via one or more NixOS test(s) if existing and applicable for the change (look inside nixos/tests)
  • Tested compilation of all pkgs that depend on this change using nix-shell -p nox --run "nox-review wip"
  • Tested execution of all binary files (usually in ./result/bin/)
  • Determined the impact on package closure size (by running nix path-info -S before and after)
  • Fits CONTRIBUTING.md.

@jtojnar
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jtojnar commented Jul 31, 2018

It would be preferable to package the dependncies in redist and use them instead of awkwardly patching them in postFixup.

@jbedo
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jbedo commented Jul 31, 2018

I agree in general, however in this case the awkward patch would still remain (albeit applied at a different time) as it is hardcoded into pyflow. It would obviate the need to recompile the file after the patch, though.

As for splitting out the packages in redist, some of them already do exist in nixpkgs. However, in the interest of reproducible science I'm hesitant to use this over the bundled code: when we write in a paper that strelka 2.9.5 was used to call variants, it should be as close to the release of Illumina as possible.

Is it preferable to split out the compilation of the redist packages as separate expressions in a let binding for the strelka package and then hack the cmake system to use these instead? I'm not sure this improves anything, it's just making nix build them instead of cmake.

@joachifm
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@GrahamcOfBorg build strelka

@GrahamcOfBorg
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Failure on aarch64-linux (full log)

Attempted: strelka

Partial log (click to expand)

  Failed to build boost library 1.58.0.  See build log:
  /build/source/build/bootstrap/boost/boost.build.error.txt
Call Stack (most recent call first):
  CMakeLists.txt:209 (include)


-- Configuring incomplete, errors occurred!
See also "/build/source/build/CMakeFiles/CMakeOutput.log".
builder for '/nix/store/lvv7cj9i7dizgakzi48xfd1n7dnc20lf-strelka-2.9.5.drv' failed with exit code 1
error: build of '/nix/store/lvv7cj9i7dizgakzi48xfd1n7dnc20lf-strelka-2.9.5.drv' failed

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Failure on x86_64-darwin (full log)

Attempted: strelka

Partial log (click to expand)

[  0%] Built target strelka_buildtime_config
Scanning dependencies of target strelka_cxx_buildtime_config
[  0%] Built target strelka_cxx_buildtime_config
Scanning dependencies of target strelka_bgzfx
[  0%] Building bgzf_extras
make[2]: *** [redist/CMakeFiles/strelka_bgzfx.dir/build.make:63: redist/bgzf_extras-v0.1/bgzf_cat] Error 2
make[1]: *** [CMakeFiles/Makefile2:209: redist/CMakeFiles/strelka_bgzfx.dir/all] Error 2
make: *** [Makefile:141: all] Error 2
builder for '/nix/store/601swdzp9i310r4kkpshx4dh0x574bdw-strelka-2.9.5.drv' failed with exit code 2
error: build of '/nix/store/601swdzp9i310r4kkpshx4dh0x574bdw-strelka-2.9.5.drv' failed

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Success on x86_64-linux (full log)

Attempted: strelka

Partial log (click to expand)

/nix/store/yfp0xxr0khxfj1kfh6a063xchm84b1c6-strelka-2.9.5/libexec/updateNoPassedVariantGTsFilter.py: interpreter directive changed from "/usr/bin/env python2" to "/nix/store/f01rhaxdfip9c49k4mhfjgfrwl5lcamn-python-2.7.15/bin/python2"
/nix/store/yfp0xxr0khxfj1kfh6a063xchm84b1c6-strelka-2.9.5/libexec/vcfCmdlineSwapper.py: interpreter directive changed from "/usr/bin/env python2" to "/nix/store/f01rhaxdfip9c49k4mhfjgfrwl5lcamn-python-2.7.15/bin/python2"
/nix/store/yfp0xxr0khxfj1kfh6a063xchm84b1c6-strelka-2.9.5/bin/runStrelkaSomaticWorkflowDemo.bash: interpreter directive changed from "/usr/bin/env bash" to "/nix/store/79b6s2wql94lwk8dyib2jc4fq8ixl13f-bash-4.4-p23/bin/bash"
/nix/store/yfp0xxr0khxfj1kfh6a063xchm84b1c6-strelka-2.9.5/bin/configureStrelkaSomaticWorkflow.py: interpreter directive changed from "/usr/bin/env python2" to "/nix/store/f01rhaxdfip9c49k4mhfjgfrwl5lcamn-python-2.7.15/bin/python2"
/nix/store/yfp0xxr0khxfj1kfh6a063xchm84b1c6-strelka-2.9.5/bin/configureStrelkaGermlineWorkflow.py: interpreter directive changed from "/usr/bin/env python2" to "/nix/store/f01rhaxdfip9c49k4mhfjgfrwl5lcamn-python-2.7.15/bin/python2"
/nix/store/yfp0xxr0khxfj1kfh6a063xchm84b1c6-strelka-2.9.5/bin/runStrelkaGermlineWorkflowDemo.bash: interpreter directive changed from "/usr/bin/env bash" to "/nix/store/79b6s2wql94lwk8dyib2jc4fq8ixl13f-bash-4.4-p23/bin/bash"
checking for references to /build in /nix/store/yfp0xxr0khxfj1kfh6a063xchm84b1c6-strelka-2.9.5...
/nix/store/yfp0xxr0khxfj1kfh6a063xchm84b1c6-strelka-2.9.5/lib/python/pyflow /build/source/build
/build/source/build
/nix/store/yfp0xxr0khxfj1kfh6a063xchm84b1c6-strelka-2.9.5

@jbedo
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jbedo commented Aug 19, 2018

I have changed platforms to only x86_64-linux.

@joachifm joachifm merged commit 6755ab8 into NixOS:master Aug 20, 2018
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@jbedo @jtojnar @joachifm @GrahamcOfBorg