Merge pull request #108943 from fabaff/bump-dnachisel

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Sandro 2021-01-12 23:41:10 +01:00 committed by GitHub
commit e354a9b386
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4 changed files with 99 additions and 8 deletions

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@ -1,21 +1,27 @@
{ lib
, buildPythonPackage
, fetchPypi
, fetchFromGitHub
, biopython
, docopt
, flametree
, numpy
, proglog
, pytestCheckHook
, python-codon-tables
}:
, primer3
, genome-collector
, matplotlib
}:
buildPythonPackage rec {
pname = "dnachisel";
version = "3.2.5";
version = "3.2.6";
src = fetchPypi {
inherit pname version;
sha256 = "35301c5eda0baca5902403504e0b5a22eb65da92c2bbd23199d95c4a6bf0ef37";
src = fetchFromGitHub {
owner = "Edinburgh-Genome-Foundry";
repo = "DnaChisel";
rev = "v${version}";
sha256 = "0m88biw7sycjwsmncdybj9n3yf4n9cyvifv9zv7irm8ha3scchji";
};
propagatedBuildInputs = [
@ -27,9 +33,24 @@ buildPythonPackage rec {
python-codon-tables
];
# no tests in tarball
doCheck = false;
checkInputs = [
primer3
genome-collector
matplotlib
pytestCheckHook
];
# Disable tests which requires network access
disabledTests = [
"test_circular_sequence_optimize_with_report"
"test_constraints_reports"
"test_optimize_with_report"
"test_optimize_with_report_no_solution"
"test_avoid_blast_matches_with_list"
"test_avoid_phage_blast_matches"
"test_avoid_matches_with_list"
"test_avoid_matches_with_phage"
];
pythonImportsCheck = [ "dnachisel" ];
meta = with lib; {

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@ -0,0 +1,34 @@
{ lib
, buildPythonPackage
, appdirs
, biopython
, fetchPypi
, proglog
}:
buildPythonPackage rec {
pname = "genome_collector";
version = "0.1.6";
src = fetchPypi {
inherit pname version;
sha256 = "0023ihrz0waxbhq28xh1ymvk51ih882y9psg4glm6s9d1zmqvdph";
};
propagatedBuildInputs = [
appdirs
biopython
proglog
];
# Project hasn't released the tests yet
doCheck = false;
pythonImportsCheck = [ "genome_collector" ];
meta = with lib; {
description = "Genomes and build BLAST/Bowtie indexes in Python";
homepage = "https://github.com/Edinburgh-Genome-Foundry/genome_collector";
license = with licenses; [ mit ];
maintainers = with maintainers; [ fab ];
};
}

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@ -0,0 +1,32 @@
{ lib
, buildPythonPackage
, fetchFromGitHub
, cython
, click
}:
buildPythonPackage rec {
pname = "primer3";
version = "0.6.1";
src = fetchFromGitHub {
owner = "libnano";
repo = "primer3-py";
rev = version;
sha256 = "1glybwp9w2m1ydvaphr41gj31d8fvlh40s35galfbjqa563si72g";
};
nativeBuildInputs = [ cython ];
# pytestCheckHook leads to a circular import issue
checkInputs = [ click ];
pythonImportsCheck = [ "primer3" ];
meta = with lib; {
description = "Oligo analysis and primer design";
homepage = "https://github.com/libnano/primer3-py";
license = with licenses; [ gpl2Only ];
maintainers = with maintainers; [ fab ];
};
}

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@ -2433,6 +2433,8 @@ in {
genanki = callPackage ../development/python-modules/genanki { };
genome-collector = callPackage ../development/python-modules/genome-collector { };
genpy = callPackage ../development/python-modules/genpy { };
genshi = callPackage ../development/python-modules/genshi { };
@ -4928,6 +4930,8 @@ in {
else
callPackage ../development/python-modules/prettytable/1.nix { };
primer3 = callPackage ../development/python-modules/primer3 { };
priority = callPackage ../development/python-modules/priority { };
prison = callPackage ../development/python-modules/prison { };