diff options
author | Robert Scott <code@humanleg.org.uk> | 2020-09-19 14:04:52 +0100 |
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committer | Robert Scott <code@humanleg.org.uk> | 2020-09-20 12:25:17 +0100 |
commit | ecd588683028b29c92c61b9f1cf685431482efd4 (patch) | |
tree | 8e414abfdecd439ea8e68eef70ad56a9e17d6bce /pkgs/applications/science/biology/truvari | |
parent | e61102d5c24b103d7eb075efa9c36f064c19d82d (diff) |
truvari: 1.3.4 -> 2.0.2, fixing build
seeing it has no tests, use pythonImportsCheck in an attempt to detect total breakage, even though it's not intended to be used as an importable module
Diffstat (limited to 'pkgs/applications/science/biology/truvari')
-rw-r--r-- | pkgs/applications/science/biology/truvari/default.nix | 19 |
1 files changed, 10 insertions, 9 deletions
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"; |