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Merge pull request #98283 from risicle/ris-truvari-2.0.2
truvari: 1.3.4 -> 2.0.2, add new dependencies & fix build
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Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,28 @@ | ||
{ stdenv | ||
, buildPythonPackage | ||
, fetchPypi | ||
, pyvcf | ||
}: | ||
|
||
buildPythonPackage rec { | ||
pname = "ACEBinf"; | ||
version = "1.0.2"; | ||
|
||
src = fetchPypi { | ||
inherit pname version; | ||
sha256 = "1168pny671l6zfm2vv1pwspnflmzi7f4v8yldjl7zlz0b9cm5zlz"; | ||
}; | ||
|
||
buildInputs = [ pyvcf ]; | ||
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# no tests | ||
doCheck = false; | ||
pythonImportsCheck = [ "acebinf" ]; | ||
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meta = with stdenv.lib; { | ||
homepage = "https://github.com/ACEnglish/acebinf"; | ||
description = "Collection of simple utilities used when building bioinformatics tools"; | ||
license = licenses.unlicense; | ||
maintainers = with maintainers; [ ris ]; | ||
}; | ||
} |
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Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,42 @@ | ||
{ stdenv | ||
, buildPythonPackage | ||
, pythonOlder | ||
, fetchPypi | ||
, bwa | ||
, cffi | ||
, zlib | ||
}: | ||
|
||
buildPythonPackage rec { | ||
pname = "bwapy"; | ||
version = "0.1.4"; | ||
disabled = pythonOlder "3.6"; | ||
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src = fetchPypi { | ||
inherit pname version; | ||
sha256 = "090qwx3vl729zn3a7sksbviyg04kc71gpbm3nd8dalqp673x1npw"; | ||
}; | ||
postPatch = '' | ||
# replace bundled bwa | ||
rm -r bwa/* | ||
cp ${bwa}/lib/*.a ${bwa}/include/*.h bwa/ | ||
substituteInPlace setup.py \ | ||
--replace 'setuptools>=49.2.0' 'setuptools' | ||
''; | ||
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buildInputs = [ zlib bwa ]; | ||
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propagatedBuildInputs = [ cffi ]; | ||
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# no tests | ||
doCheck = false; | ||
pythonImportsCheck = [ "bwapy" ]; | ||
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meta = with stdenv.lib; { | ||
homepage = "https://github.com/ACEnglish/acebinf"; | ||
description = "Python bindings to bwa mem aligner"; | ||
license = licenses.mpl20; | ||
maintainers = with maintainers; [ ris ]; | ||
}; | ||
} |
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Original file line number | Diff line number | Diff line change |
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@@ -0,0 +1,32 @@ | ||
{ stdenv | ||
, buildPythonPackage | ||
, isPy3k | ||
, fetchPypi | ||
, zlib | ||
}: | ||
|
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buildPythonPackage rec { | ||
pname = "pytabix"; | ||
version = "0.1"; | ||
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src = fetchPypi { | ||
inherit pname version; | ||
sha256 = "1ldp5r4ggskji6qx4bp2qxy2vrvb3fam03ksn0gq2hdxgrlg2x07"; | ||
}; | ||
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buildInputs = [ zlib ]; | ||
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doCheck = !isPy3k; | ||
preCheck = '' | ||
substituteInPlace test/test.py \ | ||
--replace 'test_remote_file' 'dont_test_remote_file' | ||
''; | ||
pythonImportsCheck = [ "tabix" ]; | ||
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||
meta = with stdenv.lib; { | ||
homepage = "https://github.com/slowkow/pytabix"; | ||
description = "Python interface for tabix"; | ||
license = licenses.mit; | ||
maintainers = with maintainers; [ ris ]; | ||
}; | ||
} |
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