snakemake: 8.19.3 -> 8.20.1
This commit is contained in:
Dmitry Kalinkin
@@ -1,67 +0,0 @@
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{ fetchurl }:
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{
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"snakemake/LICENSE.md" = fetchurl {
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url = "https://raw.githubusercontent.com/snakemake/snakemake/main/LICENSE.md";
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sha256 = "84a1a82b05c80637744d3fe8257235c15380efa6cc32608adf4b21f17af5d2b8";
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};
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"pygments/LICENSE" = fetchurl {
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url = "https://raw.githubusercontent.com/pygments/pygments/master/LICENSE";
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sha256 = "a9d66f1d526df02e29dce73436d34e56e8632f46c275bbdffc70569e882f9f17";
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};
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"tailwindcss/LICENSE" = fetchurl {
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url = "https://raw.githubusercontent.com/tailwindlabs/tailwindcss/master/LICENSE";
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sha256 = "60e0b68c0f35c078eef3a5d29419d0b03ff84ec1df9c3f9d6e39a519a5ae7985";
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};
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"tailwindcss/tailwind.css" = fetchurl {
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url = "https://cdn.tailwindcss.com/3.0.23?plugins=forms@0.4.0,typography@0.5.2";
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sha256 = "8a597dc918fb62e05db23a5f810327a045a62c57cfda16646075138a6ac696fa";
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};
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"react/LICENSE" = fetchurl {
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url = "https://raw.githubusercontent.com/facebook/react/main/LICENSE";
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sha256 = "da6d3703ed11cbe42bd212c725957c98da23cbff1998c05fa4b3d976d1a58e93";
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};
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"react/react.production.min.js" = fetchurl {
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url = "https://cdnjs.cloudflare.com/ajax/libs/react/18.2.0/umd/react.production.min.js";
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sha256 = "4b4969fa4ef3594324da2c6d78ce8766fbbc2fd121fff395aedf997db0a99a06";
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};
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"react/react-dom.production.min.js" = fetchurl {
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url = "https://cdnjs.cloudflare.com/ajax/libs/react-dom/18.2.0/umd/react-dom.production.min.js";
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sha256 = "21758ed084cd0e37e735722ee4f3957ea960628a29dfa6c3ce1a1d47a2d6e4f7";
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};
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"vega/vega.js" = fetchurl {
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url = "https://cdnjs.cloudflare.com/ajax/libs/vega/5.21.0/vega.js";
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sha256 = "b34c43055ef5d39a093e937522955dc359fbaec6c5b0259ae2de4c9da698e9fe";
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};
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"vega/LICENSE" = fetchurl {
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url = "https://raw.githubusercontent.com/vega/vega/main/LICENSE";
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sha256 = "63727832aaf62004a2b249c933e327f3c90caf49e41a72f4bf436edf632cbda8";
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};
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"vega-lite/vega-lite.js" = fetchurl {
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url = "https://cdnjs.cloudflare.com/ajax/libs/vega-lite/5.2.0/vega-lite.js";
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sha256 = "6eb7f93121cd9f44cf8640244f87c5e143f87c7a0b6cd113da4a9e41e3adf0aa";
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};
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"vega-lite/LICENSE" = fetchurl {
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url = "https://raw.githubusercontent.com/vega/vega-lite/next/LICENSE";
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sha256 = "f618900fd0d64046963b29f40590cdd1e341a2f41449f99110d82fd81fea808c";
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};
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"vega-embed/vega-embed.js" = fetchurl {
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url = "https://cdnjs.cloudflare.com/ajax/libs/vega-embed/6.20.8/vega-embed.js";
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sha256 = "4e546c1f86eb200333606440e92f76e2940b905757018d9672cd1708e4e6ff0a";
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};
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"vega-embed/LICENSE" = fetchurl {
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url = "https://raw.githubusercontent.com/vega/vega-embed/next/LICENSE";
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sha256 = "32df67148f0fc3db0eb9e263a7b75d07f1eb14c61955005a4a39c6918d10d137";
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};
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"heroicons/LICENSE" = fetchurl {
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url = "https://raw.githubusercontent.com/tailwindlabs/heroicons/master/LICENSE";
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sha256 = "60e0b68c0f35c078eef3a5d29419d0b03ff84ec1df9c3f9d6e39a519a5ae7985";
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};
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"prop-types/prop-types.min.js" = fetchurl {
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url = "https://cdnjs.cloudflare.com/ajax/libs/prop-types/15.7.2/prop-types.min.js";
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sha256 = "4c88350517ee82aa4f3368e67ef1a453ca6636dcfa6449b4e3d6faa5c877066e";
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};
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"prop-types/LICENSE" = fetchurl {
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url = "https://raw.githubusercontent.com/facebook/prop-types/main/LICENSE";
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sha256 = "f657f99d3fb9647db92628e96007aabb46e5f04f33e49999075aab8e250ca7ce";
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};
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}
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@@ -1,9 +0,0 @@
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/Asset(.*/ { # find Asset declaration
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s/: Asset(/ = fetchurl {/; # replace leading
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:b; # a label
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$!N; # if not EOF, include next line
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s/",/";/; # provide separators between attributes
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/)/!bb; # repeat until a closing bracket is located
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s/),/};/; # provide separators between assets
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p # output what we have
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}
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@@ -1,7 +1,6 @@
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{ lib
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, fetchFromGitHub
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, fetchPypi
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, fetchpatch
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, fetchurl
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, python3
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, runtimeShell
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, stress
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@@ -9,29 +8,14 @@
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python3.pkgs.buildPythonApplication rec {
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pname = "snakemake";
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version = "8.19.3";
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version = "8.20.1";
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format = "setuptools";
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src = fetchFromGitHub {
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owner = "snakemake";
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repo = pname;
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rev = "refs/tags/v${version}";
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hash = "sha256-DWlMF/aNRCYDfTP41ALaGJFBTBjHxqZtx/0PtD/37KY=";
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# https://github.com/python-versioneer/python-versioneer/issues/217
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postFetch = ''
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sed -i "$out"/snakemake/_version.py -e 's#git_refnames = ".*"#git_refnames = " (tag: v${version})"#'
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'';
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src = fetchPypi {
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inherit pname version;
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hash = "sha256-adNwIA1z/TwWsa0gQb4hAsUvHInjd30sm1dYKXvvXy8=";
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};
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patches = [
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# Avoid downloading if files are provided
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# https://github.com/snakemake/snakemake/pull/3072
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(fetchpatch {
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url = "https://github.com/snakemake/snakemake/commit/ea89ec2f20faa0db303fdab0eafa640c9147cc14.diff";
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hash = "sha256-gzmto3Kusk40kPH29DkvYcJgAx2VAOq3mw5vPSCp5mI=";
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})
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];
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postPatch = ''
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patchShebangs --build tests/
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substituteInPlace tests/common.py \
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@@ -39,14 +23,7 @@ python3.pkgs.buildPythonApplication rec {
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--replace-fail 'del os.environ["PYTHONPATH"]' "pass"
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substituteInPlace snakemake/unit_tests/__init__.py \
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--replace-fail '"unit_tests/templates"' '"'"$PWD"'/snakemake/unit_tests/templates"'
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'' + (let
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assets = import ./assets.nix { inherit fetchurl; };
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in
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# Use fetchPypi once https://github.com/snakemake/snakemake/pull/3073 is available
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lib.concatStrings (lib.mapAttrsToList (name: file: ''
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echo install -D "${file}" snakemake/assets/data/${name}
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install -D "${file}" snakemake/assets/data/${name}
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'') assets));
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'';
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propagatedBuildInputs = with python3.pkgs; [
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appdirs
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@@ -106,44 +83,6 @@ python3.pkgs.buildPythonApplication rec {
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# Some will be disabled via https://github.com/snakemake/snakemake/pull/3074
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disabledTests = [
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# requires network connection
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"test_deploy_sources"
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"test_modules_meta_wrapper"
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"test_module_complex"
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"test_module_complex2"
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"test_module_with_script"
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"test_module_report"
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"test_load_metawrapper"
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# requires conda
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"test_archive"
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"test_script"
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"test_conda"
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"test_conda_list_envs"
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"test_upstream_conda"
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"test_deploy_script"
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"test_deploy_hashing"
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"test_conda_custom_prefix"
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"test_conda_cmd_exe"
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"test_wrapper"
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"test_wrapper_local_git_prefix"
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"test_singularity_conda"
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"test_issue635"
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"test_issue1093"
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"test_jupyter_notebook"
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"test_jupyter_notebook_draft"
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"test_converting_path_for_r_script"
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"test_conda_named"
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"test_conda_function"
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"test_conda_pin_file"
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"test_conda_python_script"
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"test_conda_python_3_7_script"
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"test_prebuilt_conda_script"
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"test_conda_global"
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"test_script_pre_py39"
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"test_resource_string_in_cli_or_profile"
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"test_conda"
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"test_env_modules"
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"test_script_pre_py39"
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# requires graphviz
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"test_filegraph"
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# requires s3
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@@ -152,28 +91,23 @@ python3.pkgs.buildPythonApplication rec {
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"test_output_file_cache_storage"
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# requires peppy and eido
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"test_pep"
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"test_modules_peppy"
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# requires perl
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"test_shadow"
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# requires snakemake-storage-plugin-http
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"test_ancient"
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"test_modules_prefix"
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# requires snakemake-storage-plugin-s3
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"test_deploy_sources"
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# requires modules
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"test_env_modules"
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# issue with locating template file
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"test_generate_unit_tests"
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# weird
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"test_strict_mode"
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"test_issue1256"
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"test_issue2574"
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# requires apptainer
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"test_singularity"
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"test_singularity_cluster"
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"test_singularity_invalid"
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"test_singularity_module_invalid"
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"test_singularity_none"
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"test_singularity_global"
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"test_cwl_singularity"
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"test_issue1083"
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"test_github_issue78"
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"test_container"
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"test_shell_exec"
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"test_containerized"
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"test_github_issue1384"
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# future-proofing
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"conda"
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"singularity"
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@@ -189,8 +123,6 @@ python3.pkgs.buildPythonApplication rec {
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export HOME="$(mktemp -d)"
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'';
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passthru.updateScript = ./update.sh;
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meta = with lib; {
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homepage = "https://snakemake.github.io";
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license = licenses.mit;
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@@ -1,21 +0,0 @@
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#!/usr/bin/env nix-shell
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#!nix-shell -i bash -p curl common-updater-scripts gnused nixfmt-rfc-style
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set -eu -o pipefail
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version=${1:-$(curl -s https://api.github.com/repos/snakemake/snakemake/releases/latest | jq --raw-output '.tag_name[1:]')}
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update-source-version snakemake $version
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basedir="$(dirname "$0")"
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cat <<EOF > "$basedir/assets.nix"
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{ fetchurl }:
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{
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EOF
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outlink="$basedir/src"
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nix-build . -A snakemake.src -o "$outlink"
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sed "$outlink"/snakemake/assets/__init__.py -n -f "$basedir/assets.sed" >> "$basedir/assets.nix"
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rm "$outlink"
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cat <<EOF >> "$basedir/assets.nix"
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}
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EOF
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nixfmt "$basedir/assets.nix"
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