Merge pull request #45730 from Helkafen/snakemake

snakemake: init at 5.2.2
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Ryan Mulligan 2018-09-02 07:54:13 -07:00 committed by GitHub
commit 7b54a50e97
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5 changed files with 85 additions and 0 deletions

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@ -1645,6 +1645,11 @@
github = "heel";
name = "Sergii Paryzhskyi";
};
helkafen = {
email = "arnaudpourseb@gmail.com";
github = "Helkafen";
name = "Sébastian Méric de Bellefon";
};
henrytill = {
email = "henrytill@gmail.com";
github = "henrytill";

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@ -0,0 +1,41 @@
{
stdenv
, python
}:
python.buildPythonPackage rec {
pname = "snakemake";
version = "5.2.2";
propagatedBuildInputs = with python; [
appdirs
ConfigArgParse
datrie
docutils
jsonschema
pyyaml
ratelimiter
requests
wrapt
];
src = python.fetchPypi {
inherit pname version;
sha256 = "adffe7e24b4a613a9e8bf0a2a320b3cea236d86afb9132bb0bbbc08b8e35a3a3";
};
doCheck = false; # Tests depend on Google Cloud credentials at ${HOME}/gcloud-service-key.json
meta = with stdenv.lib; {
homepage = http://snakemake.bitbucket.io;
license = licenses.mit;
description = "Python-based execution environment for make-like workflows";
longDescription = ''
Snakemake is a workflow management system that aims to reduce the complexity of
creating workflows by providing a fast and comfortable execution environment,
together with a clean and readable specification language in Python style. Snakemake
workflows are essentially Python scripts extended by declarative code to define
rules. Rules describe how to create output files from input files.
'';
};
}

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@ -0,0 +1,35 @@
{
stdenv
, buildPythonPackage
, fetchPypi
, pytest
, glibcLocales
}:
buildPythonPackage rec {
pname = "ratelimiter";
version = "1.2.0.post0";
src = fetchPypi {
inherit pname version;
sha256 = "5c395dcabdbbde2e5178ef3f89b568a3066454a6ddc223b76473dac22f89b4f7";
};
LC_ALL = "en_US.utf-8";
nativeBuildInputs = [ glibcLocales ];
checkInputs = [ pytest ];
checkPhase = ''
py.test tests
'';
meta = with stdenv.lib; {
homepage = https://github.com/RazerM/ratelimiter;
license = licenses.asl20;
description = "Simple python rate limiting object";
maintainers = with maintainers; [ helkafen ];
};
}

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@ -8685,6 +8685,8 @@ with pkgs;
smc = callPackage ../tools/misc/smc { };
snakemake = callPackage ../applications/science/misc/snakemake { python = python3Packages; };
snowman = qt5.callPackage ../development/tools/analysis/snowman { };
sparse = callPackage ../development/tools/analysis/sparse { };

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@ -4347,6 +4347,8 @@ in {
regex = callPackage ../development/python-modules/regex { };
ratelimiter = callPackage ../development/python-modules/ratelimiter { };
repoze_lru = buildPythonPackage rec {
name = "repoze.lru-0.6";