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nixpkgs/pkgs/applications/science/misc/snakemake/default.nix

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treewide: remove stdenv where not needed
2021-01-25 08:26:54 +00:00
{ lib, python3Packages }:
python.pkgs.snakemake: init at 5.2.2
2018-08-29 15:27:05 +01:00
snakemake: 5.4.4 -> 5.7.4 (#72929) (#72929)
2019-11-12 23:46:56 +00:00
python3Packages.buildPythonApplication rec {
python.pkgs.snakemake: init at 5.2.2
2018-08-29 15:27:05 +01:00
pname = "snakemake";
snakemake: 6.5.0 -> 6.5.3
2021-07-11 15:40:09 +01:00
version = "6.5.3";
python.pkgs.snakemake: init at 5.2.2
2018-08-29 15:27:05 +01:00
snakemake: 5.4.4 -> 5.7.4 (#72929) (#72929)
2019-11-12 23:46:56 +00:00
propagatedBuildInputs = with python3Packages; [
python.pkgs.snakemake: init at 5.2.2
2018-08-29 15:27:05 +01:00
appdirs
ConfigArgParse
snakemake: 6.0.5 -> 6.5.0
2021-06-22 22:18:35 +01:00
connection-pool
python.pkgs.snakemake: init at 5.2.2
2018-08-29 15:27:05 +01:00
datrie
docutils
snakemake: 5.28.0 -> 6.0.5
2021-03-26 22:32:26 +00:00
filelock
snakemake: 5.2.2 -> 5.4.4
2019-04-10 19:18:26 +01:00
GitPython
python.pkgs.snakemake: init at 5.2.2
2018-08-29 15:27:05 +01:00
jsonschema
snakemake: 5.9.1 -> 5.10.0
2020-03-14 20:59:46 +00:00
nbformat
snakemake: 5.4.4 -> 5.7.4 (#72929) (#72929)
2019-11-12 23:46:56 +00:00
psutil
snakemake: 5.19.3 -> 5.28.0
2020-11-17 22:37:35 +00:00
pulp
python.pkgs.snakemake: init at 5.2.2
2018-08-29 15:27:05 +01:00
pyyaml
ratelimiter
requests
pythonPackages.smart_open: rename to smart-open
2021-03-15 00:01:41 +00:00
smart-open
snakemake: 6.0.5 -> 6.5.0
2021-06-22 22:18:35 +01:00
stopit
tabulate
snakemake: 5.9.1 -> 5.10.0
2020-03-14 20:59:46 +00:00
toposort
python.pkgs.snakemake: init at 5.2.2
2018-08-29 15:27:05 +01:00
wrapt
];
snakemake: 5.4.4 -> 5.7.4 (#72929) (#72929)
2019-11-12 23:46:56 +00:00
src = python3Packages.fetchPypi {
python.pkgs.snakemake: init at 5.2.2
2018-08-29 15:27:05 +01:00
inherit pname version;
snakemake: 6.5.0 -> 6.5.3
2021-07-11 15:40:09 +01:00
sha256 = "a06839346425c74542e6e2e6047db3133cd747ef89e1ebd87dad1fbba041f62d";
python.pkgs.snakemake: init at 5.2.2
2018-08-29 15:27:05 +01:00
};
doCheck = false; # Tests depend on Google Cloud credentials at ${HOME}/gcloud-service-key.json
treewide: with stdenv.lib; in meta -> with lib; Part of: https://github.com/NixOS/nixpkgs/issues/108938 meta = with stdenv.lib; is a widely used pattern. We want to slowly remove the `stdenv.lib` indirection and encourage people to use `lib` directly. Thus let’s start with the meta field. This used a rewriting script to mostly automatically replace all occurances of this pattern, and add the `lib` argument to the package header if it doesn’t exist yet. The script in its current form is available at https://cs.tvl.fyi/depot@2f807d7f141068d2d60676a89213eaa5353ca6e0/-/blob/users/Profpatsch/nixpkgs-rewriter/default.nix
2021-01-11 07:54:33 +00:00
meta = with lib; {
snakemake: 5.28.0 -> 6.0.5
2021-03-26 22:32:26 +00:00
homepage = "https://snakemake.github.io";
python.pkgs.snakemake: init at 5.2.2
2018-08-29 15:27:05 +01:00
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.
'';
snakemake: 5.9.1 -> 5.10.0
2020-03-14 20:59:46 +00:00
maintainers = with maintainers; [ helkafen renatoGarcia veprbl ];
python.pkgs.snakemake: init at 5.2.2
2018-08-29 15:27:05 +01:00
};
}
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