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hisat2: init 2.1.0 #45102

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merged 1 commit into from Sep 10, 2018
Merged

hisat2: init 2.1.0 #45102

merged 1 commit into from Sep 10, 2018

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jbedo
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@jbedo jbedo commented Aug 16, 2018

Motivation for this change
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.

mpickering
mpickering reviewed Aug 16, 2018
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pkgs/applications/science/biology/hisat2/default.nix Outdated
version = "2.1.0";

src = fetchFromGitHub {
owner = "infphilo";
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Why do you not get the source from the official release tarball?

ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/downloads

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I don't think this is any more "official" since they link to both the tarball and their github page for source. I have no strong desire to use github over the tarball, so I've switched to the tarball.

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@GrahamcOfBorg build hisat2

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Failure on aarch64-linux (full log)

Attempted: hisat2

Partial log (click to expand)

 -I third_party \
-o hisat2-build-s hisat2_build.cpp \
ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp diff_sample.cpp hisat2_build_main.cpp \
-lpthread
/nix/store/7q3ayirslrcva28wava6zpjcflcz1h3b-bash-4.4-p23/bin/bash: hostname: command not found
g++: error: unrecognized command line option '-m32'
g++: error: unrecognized command line option '-msse2'
make: *** [Makefile:275: hisat2-build-s] Error 1
builder for '/nix/store/5x70gn8zbfww8f1hzvjd8yawrd2z9yxa-hisat2-2.1.0.drv' failed with exit code 2
error: build of '/nix/store/5x70gn8zbfww8f1hzvjd8yawrd2z9yxa-hisat2-2.1.0.drv' failed

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Success on x86_64-linux (full log)

Attempted: hisat2

Partial log (click to expand)

/nix/store/k398a1i35li0racraydnfwag778kdq5j-hisat2-2.1.0/bin/extract_exons.py: interpreter directive changed from "/usr/bin/env python" to "/nix/store/9qjc0d5557h3dkpsvfq98b2k96lnb6pw-python-2.7.15/bin/python"
/nix/store/k398a1i35li0racraydnfwag778kdq5j-hisat2-2.1.0/bin/hisatgenotype_extract_reads.py: interpreter directive changed from "/usr/bin/env python" to "/nix/store/9qjc0d5557h3dkpsvfq98b2k96lnb6pw-python-2.7.15/bin/python"
/nix/store/k398a1i35li0racraydnfwag778kdq5j-hisat2-2.1.0/bin/hisat2-inspect: interpreter directive changed from "/usr/bin/env python" to "/nix/store/9qjc0d5557h3dkpsvfq98b2k96lnb6pw-python-2.7.15/bin/python"
/nix/store/k398a1i35li0racraydnfwag778kdq5j-hisat2-2.1.0/bin/hisat2_simulate_reads.py: interpreter directive changed from "/usr/bin/env python" to "/nix/store/9qjc0d5557h3dkpsvfq98b2k96lnb6pw-python-2.7.15/bin/python"
/nix/store/k398a1i35li0racraydnfwag778kdq5j-hisat2-2.1.0/bin/hisat2_extract_snps_haplotypes_VCF.py: interpreter directive changed from "/usr/bin/env python" to "/nix/store/9qjc0d5557h3dkpsvfq98b2k96lnb6pw-python-2.7.15/bin/python"
/nix/store/k398a1i35li0racraydnfwag778kdq5j-hisat2-2.1.0/bin/hisatgenotype.py: interpreter directive changed from "/usr/bin/env python" to "/nix/store/9qjc0d5557h3dkpsvfq98b2k96lnb6pw-python-2.7.15/bin/python"
/nix/store/k398a1i35li0racraydnfwag778kdq5j-hisat2-2.1.0/bin/hisat2_extract_snps_haplotypes_UCSC.py: interpreter directive changed from "/usr/bin/env python" to "/nix/store/9qjc0d5557h3dkpsvfq98b2k96lnb6pw-python-2.7.15/bin/python"
/nix/store/k398a1i35li0racraydnfwag778kdq5j-hisat2-2.1.0/bin/hisat2_extract_splice_sites.py: interpreter directive changed from "/usr/bin/env python" to "/nix/store/9qjc0d5557h3dkpsvfq98b2k96lnb6pw-python-2.7.15/bin/python"
checking for references to /build in /nix/store/k398a1i35li0racraydnfwag778kdq5j-hisat2-2.1.0...
/nix/store/k398a1i35li0racraydnfwag778kdq5j-hisat2-2.1.0

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Failure on x86_64-darwin (full log)

Attempted: hisat2

Partial log (click to expand)

dirname: missing operand
Try 'dirname --help' for more information.
which: no gcc in (/nix/store/f6f3dhwjbi0mwcmd45g89094alxp40li-clang-wrapper-5.0.2/bin:/nix/store/7mkcfjzlzgycc6b7n5d3lmcal7v42vdy-clang-5.0.2/bin:/nix/store/ky1iq8hmr1b958d8fcaggpyaxhnfa8a6-coreutils-8.29/bin:/nix/store/9a574dabc03ywm48r42n5a2qd28gjl7p-cctools-binutils-darwin-wrapper/bin:/nix/store/251fvx4mx9q4zarbca5cciasmn66p668-cctools-binutils-darwin/bin:/nix/store/ky1iq8hmr1b958d8fcaggpyaxhnfa8a6-coreutils-8.29/bin:/nix/store/5h0lxbjam7z8kacazb3a25kbm11mxsrs-unzip-6.0/bin:/nix/store/95ifvh2cpawnfnjmp9ayr2f76vnskfl2-which-2.21/bin:/nix/store/lcb5fjx5qind424zfx8adrd3f1rn5xar-python-2.7.15/bin:/nix/store/ky1iq8hmr1b958d8fcaggpyaxhnfa8a6-coreutils-8.29/bin:/nix/store/9yc3xws4p54jyz5x5rf3cmmzyrlaqilj-findutils-4.6.0/bin:/nix/store/nh3adr5j6lvnxzwksiv064av80yqsryn-diffutils-3.6/bin:/nix/store/37k5czxj6c5zywrps0g8rqffbb7rhk0v-gnused-4.5/bin:/nix/store/4p1nydd81j03rxph6sjmvz0bq4qhmk1z-gnugrep-3.1/bin:/nix/store/23s49px17hh4qm89hysfgb0wrrkv2dpn-gawk-4.2.1/bin:/nix/store/5xncf6skingfyi78s112scm1mzj665v2-gnutar-1.30/bin:/nix/store/xx1qf80hv4x4hq21x29qfgml2qnahbbf-gzip-1.9/bin:/nix/store/zd53gw51jnlpz0f11hk8a7k68kjgs64c-bzip2-1.0.6.0.1-bin/bin:/nix/store/6jdrczbr2haw6yw10m5xg5mxksxbhfiy-gnumake-4.2.1/bin:/nix/store/hp9yq2m1i066irvasv20zr2lmj54fk9h-bash-4.4-p23/bin:/nix/store/q14z5idmqr6df1fjlad27nln0a1z8dmq-patch-2.7.6/bin:/nix/store/hza5gnygk6y4nwdvkzb009baax4c3xqs-xz-5.2.4-bin/bin)
dirname: missing operand
Try 'dirname --help' for more information.
/nix/store/hp9yq2m1i066irvasv20zr2lmj54fk9h-bash-4.4-p23/bin/bash: hostname: command not found
/nix/store/hp9yq2m1i066irvasv20zr2lmj54fk9h-bash-4.4-p23/bin/bash: /g++: No such file or directory
make: *** [Makefile:275: hisat2-build-s] Error 127
builder for '/nix/store/n7bjsb033dg9n31vqp3aanpwcx1gg7vr-hisat2-2.1.0.drv' failed with exit code 2
error: build of '/nix/store/n7bjsb033dg9n31vqp3aanpwcx1gg7vr-hisat2-2.1.0.drv' failed

@mpickering
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Please fix the darwin build or modify the platforms attribute.

@jbedo jbedo force-pushed the hisat2 branch 2 times, most recently from e131a31 to a9ef705 Compare August 16, 2018 21:25
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@GrahamcOfBorg build hisat2

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No attempt on x86_64-darwin (full log)

The following builds were skipped because they don't evaluate on x86_64-darwin: hisat2

Partial log (click to expand)


a) For `nixos-rebuild` you can set
  { nixpkgs.config.allowUnsupportedSystem = true; }
in configuration.nix to override this.

b) For `nix-env`, `nix-build`, `nix-shell` or any other Nix command you can add
  { allowUnsupportedSystem = true; }
to ~/.config/nixpkgs/config.nix.

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Failure on aarch64-linux (full log)

Attempted: hisat2

Partial log (click to expand)

 -I third_party \
-o hisat2-build-s hisat2_build.cpp \
ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp diff_sample.cpp hisat2_build_main.cpp \
-lpthread
/nix/store/7q3ayirslrcva28wava6zpjcflcz1h3b-bash-4.4-p23/bin/bash: hostname: command not found
g++: error: unrecognized command line option '-m32'
g++: error: unrecognized command line option '-msse2'
make: *** [Makefile:275: hisat2-build-s] Error 1
builder for '/nix/store/ljh7r7xnrwp0bdqawb5d8vgwxky4fnmd-hisat2-2.1.0.drv' failed with exit code 2
error: build of '/nix/store/ljh7r7xnrwp0bdqawb5d8vgwxky4fnmd-hisat2-2.1.0.drv' failed

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Success on x86_64-linux (full log)

Attempted: hisat2

Partial log (click to expand)

/nix/store/f53k9kdp52b0dfwqcpl5zhfabynl6zr3-hisat2-2.1.0/bin/hisatgenotype_extract_reads.py: interpreter directive changed from "/usr/bin/env python" to "/nix/store/9qjc0d5557h3dkpsvfq98b2k96lnb6pw-python-2.7.15/bin/python"
/nix/store/f53k9kdp52b0dfwqcpl5zhfabynl6zr3-hisat2-2.1.0/bin/hisat2_extract_splice_sites.py: interpreter directive changed from "/usr/bin/env python" to "/nix/store/9qjc0d5557h3dkpsvfq98b2k96lnb6pw-python-2.7.15/bin/python"
/nix/store/f53k9kdp52b0dfwqcpl5zhfabynl6zr3-hisat2-2.1.0/bin/hisat2_extract_exons.py: interpreter directive changed from "/usr/bin/env python" to "/nix/store/9qjc0d5557h3dkpsvfq98b2k96lnb6pw-python-2.7.15/bin/python"
/nix/store/f53k9kdp52b0dfwqcpl5zhfabynl6zr3-hisat2-2.1.0/bin/hisat2-build: interpreter directive changed from "/usr/bin/env python" to "/nix/store/9qjc0d5557h3dkpsvfq98b2k96lnb6pw-python-2.7.15/bin/python"
/nix/store/f53k9kdp52b0dfwqcpl5zhfabynl6zr3-hisat2-2.1.0/bin/hisatgenotype_extract_vars.py: interpreter directive changed from "/usr/bin/env python" to "/nix/store/9qjc0d5557h3dkpsvfq98b2k96lnb6pw-python-2.7.15/bin/python"
/nix/store/f53k9kdp52b0dfwqcpl5zhfabynl6zr3-hisat2-2.1.0/bin/hisat2_extract_snps_haplotypes_UCSC.py: interpreter directive changed from "/usr/bin/env python" to "/nix/store/9qjc0d5557h3dkpsvfq98b2k96lnb6pw-python-2.7.15/bin/python"
/nix/store/f53k9kdp52b0dfwqcpl5zhfabynl6zr3-hisat2-2.1.0/bin/hisatgenotype_locus.py: interpreter directive changed from "/usr/bin/env python" to "/nix/store/9qjc0d5557h3dkpsvfq98b2k96lnb6pw-python-2.7.15/bin/python"
/nix/store/f53k9kdp52b0dfwqcpl5zhfabynl6zr3-hisat2-2.1.0/bin/extract_splice_sites.py: interpreter directive changed from "/usr/bin/env python" to "/nix/store/9qjc0d5557h3dkpsvfq98b2k96lnb6pw-python-2.7.15/bin/python"
checking for references to /build in /nix/store/f53k9kdp52b0dfwqcpl5zhfabynl6zr3-hisat2-2.1.0...
/nix/store/f53k9kdp52b0dfwqcpl5zhfabynl6zr3-hisat2-2.1.0

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jbedo commented Aug 17, 2018

Sorry keep getting the platforms slightly wrong, seems it assumes sse so has to be x86. I've tried to restrict to x86 linux only, is this the cleanest way?

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You can see the available platforms here -

nixpkgs/lib/systems/for-meta.nix

Line 9 in e4d9ce9

all = [ {} ]; # `{}` matches anything

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jbedo commented Aug 19, 2018

Thanks, doesn't look any cleaner than just listing the two platforms.

@matthewbauer matthewbauer merged commit 40d19d8 into NixOS:master Sep 10, 2018
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