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| author | Jon <jonringer@users.noreply.github.com> | 2020-09-22 23:10:58 -0700 |
|---|---|---|
| committer | GitHub <noreply@github.com> | 2020-09-22 23:10:58 -0700 |
| commit | c7fdc43709c1e31b6b46cba52ba008cdb4359a2e (patch) | |
| tree | fe53f18145a66ecc84b4689f0743bc15a45f5ea8 /pkgs/applications | |
| parent | 908d8c3459941010dfddd655116f9a23aac9670d (diff) | |
| parent | ecd588683028b29c92c61b9f1cf685431482efd4 (diff) | |
Merge pull request #98283 from risicle/ris-truvari-2.0.2
truvari: 1.3.4 -> 2.0.2, add new dependencies & fix build
Diffstat (limited to 'pkgs/applications')
| -rw-r--r-- | pkgs/applications/science/biology/bwa/default.nix | 9 | ||||
| -rw-r--r-- | pkgs/applications/science/biology/truvari/default.nix | 19 |
2 files changed, 18 insertions, 10 deletions
diff --git a/pkgs/applications/science/biology/bwa/default.nix b/pkgs/applications/science/biology/bwa/default.nix index e478c104edef9..7212b42198c41 100644 --- a/pkgs/applications/science/biology/bwa/default.nix +++ b/pkgs/applications/science/biology/bwa/default.nix @@ -11,8 +11,15 @@ stdenv.mkDerivation rec { buildInputs = [ zlib ]; + # it's unclear which headers are intended to be part of the public interface + # so we may find ourselves having to add more here over time installPhase = '' - install -vD bwa $out/bin/bwa + install -vD -t $out/bin bwa + install -vD -t $out/lib libbwa.a + install -vD -t $out/include bntseq.h + install -vD -t $out/include bwa.h + install -vD -t $out/include bwamem.h + install -vD -t $out/include bwt.h ''; meta = with stdenv.lib; { diff --git a/pkgs/applications/science/biology/truvari/default.nix b/pkgs/applications/science/biology/truvari/default.nix index 84cc9909a48dc..fffeca2c740ca 100644 --- a/pkgs/applications/science/biology/truvari/default.nix +++ b/pkgs/applications/science/biology/truvari/default.nix @@ -5,13 +5,13 @@ python3Packages.buildPythonApplication rec { pname = "truvari"; - version = "1.3.4"; + version = "2.0.2"; src = fetchFromGitHub { owner = "spiralgenetics"; repo = "truvari"; rev = "v${version}"; - sha256 = "1bph7v48s7pyfagz8a2fzl5fycjliqzn5lcbv3m2bp2ih1f1gd1v"; + sha256 = "0lp1wnldjv92k4ncga1h0icb0dpjsrx427vggg40x04a7kp9lwx0"; }; propagatedBuildInputs = with python3Packages; [ @@ -21,15 +21,16 @@ python3Packages.buildPythonApplication rec { pysam pyfaidx intervaltree + pytabix + acebinf + bwapy + joblib + pandas ]; - prePatch = '' - substituteInPlace ./setup.py \ - --replace '"progressbar2==3.41.0",' '"progressbar2",' \ - --replace '"pysam==0.15.2",' '"pysam",' \ - --replace '"pyfaidx==0.5.5.2",' '"pyfaidx",' \ - --replace '"intervaltree==3.0.2",' '"intervaltree",' - ''; + # no tests + doCheck = false; + pythonImportsCheck = [ "truvari" ]; meta = with lib; { description = "Structural variant comparison tool for VCFs"; |