snakemake 5.5.3
Closes #42059. Signed-off-by: FX Coudert <fxcoudert@gmail.com>
This commit is contained in:
Caleb Xu
FX Coudert
parent
57930c531d
commit
d587546b1b
1 changed files with 54 additions and 55 deletions
|
|
@ -1,8 +1,10 @@
|
|||
class Snakemake < Formula
|
||||
include Language::Python::Virtualenv
|
||||
|
||||
desc "Pythonic workflow system"
|
||||
homepage "https://snakemake.readthedocs.io/"
|
||||
url "https://files.pythonhosted.org/packages/5a/a5/704ff1f58a121acf8b96f13a9b0abdbbb27a1a78cf52c676bd0bbd2c5f40/snakemake-5.2.2.tar.gz"
|
||||
sha256 "adffe7e24b4a613a9e8bf0a2a320b3cea236d86afb9132bb0bbbc08b8e35a3a3"
|
||||
url "https://files.pythonhosted.org/packages/58/70/daa0a380c14016b4510f6e039b5ee6c27125b66b3867a16933aa81471091/snakemake-5.5.3.tar.gz"
|
||||
sha256 "a598d8744fa1227316e2b6b8a3710c068c087957a431325c1e4e4a363dc6b1a8"
|
||||
head "https://bitbucket.org/snakemake/snakemake.git"
|
||||
|
||||
bottle do
|
||||
|
|
@ -15,19 +17,19 @@ class Snakemake < Formula
|
|||
|
||||
depends_on "python"
|
||||
|
||||
resource "Cython" do
|
||||
url "https://files.pythonhosted.org/packages/d2/12/8ef44cede251b93322e8503fd6e1b25a0249fa498bebec191a5a06adbe51/Cython-0.28.4.tar.gz"
|
||||
sha256 "76ac2b08d3d956d77b574bb43cbf1d37bd58b9d50c04ba281303e695854ebc46"
|
||||
end
|
||||
|
||||
resource "appdirs" do
|
||||
url "https://files.pythonhosted.org/packages/48/69/d87c60746b393309ca30761f8e2b49473d43450b150cb08f3c6df5c11be5/appdirs-1.4.3.tar.gz"
|
||||
sha256 "9e5896d1372858f8dd3344faf4e5014d21849c756c8d5701f78f8a103b372d92"
|
||||
end
|
||||
|
||||
resource "attrs" do
|
||||
url "https://files.pythonhosted.org/packages/cc/d9/931a24cc5394f19383fbbe3e1147a0291276afa43a0dc3ed0d6cd9fda813/attrs-19.1.0.tar.gz"
|
||||
sha256 "f0b870f674851ecbfbbbd364d6b5cbdff9dcedbc7f3f5e18a6891057f21fe399"
|
||||
end
|
||||
|
||||
resource "certifi" do
|
||||
url "https://files.pythonhosted.org/packages/4d/9c/46e950a6f4d6b4be571ddcae21e7bc846fcbb88f1de3eff0f6dd0a6be55d/certifi-2018.4.16.tar.gz"
|
||||
sha256 "13e698f54293db9f89122b0581843a782ad0934a4fe0172d2a980ba77fc61bb7"
|
||||
url "https://files.pythonhosted.org/packages/c5/67/5d0548226bcc34468e23a0333978f0e23d28d0b3f0c71a151aef9c3f7680/certifi-2019.6.16.tar.gz"
|
||||
sha256 "945e3ba63a0b9f577b1395204e13c3a231f9bc0223888be653286534e5873695"
|
||||
end
|
||||
|
||||
resource "chardet" do
|
||||
|
|
@ -36,13 +38,13 @@ class Snakemake < Formula
|
|||
end
|
||||
|
||||
resource "ConfigArgParse" do
|
||||
url "https://files.pythonhosted.org/packages/77/61/ae928ce6ab85d4479ea198488cf5ffa371bd4ece2030c0ee85ff668deac5/ConfigArgParse-0.13.0.tar.gz"
|
||||
sha256 "e6441aa58e23d3d122055808e5e2220fd742dff6e1e51082d2a4e4ed145dd788"
|
||||
url "https://files.pythonhosted.org/packages/55/ea/f0ade52790bcd687127a302b26c1663bf2e0f23210d5281dbfcd1dfcda28/ConfigArgParse-0.14.0.tar.gz"
|
||||
sha256 "2e2efe2be3f90577aca9415e32cb629aa2ecd92078adbe27b53a03e53ff12e91"
|
||||
end
|
||||
|
||||
resource "datrie" do
|
||||
url "https://files.pythonhosted.org/packages/44/5f/bf7e4711f6aa95edb2216b3487eeac719645802259643d341668e65636db/datrie-0.7.1.tar.gz"
|
||||
sha256 "7a11371cc2dbbad71d6dfef57ced6e8b384bb377eeb847c63d58f8dc8e8b2023"
|
||||
url "https://files.pythonhosted.org/packages/f5/a2/49d6db3af61eb139fb8fa2cdff90a4789e8255d227baf8f9a1ec945b4aac/datrie-0.8.tar.gz"
|
||||
sha256 "bdd5da6ba6a97e7cd96eef2e7441c8d2ef890d04ba42694a41c7dffa3aca680c"
|
||||
end
|
||||
|
||||
resource "docutils" do
|
||||
|
|
@ -50,19 +52,34 @@ class Snakemake < Formula
|
|||
sha256 "51e64ef2ebfb29cae1faa133b3710143496eca21c530f3f71424d77687764274"
|
||||
end
|
||||
|
||||
resource "gitdb2" do
|
||||
url "https://files.pythonhosted.org/packages/c4/5c/579abccd59187eaf6b3c8a4a6ecd86fce1dfd818155bfe4c52ac28dca6b7/gitdb2-2.0.5.tar.gz"
|
||||
sha256 "83361131a1836661a155172932a13c08bda2db3674e4caa32368aa6eb02f38c2"
|
||||
end
|
||||
|
||||
resource "GitPython" do
|
||||
url "https://files.pythonhosted.org/packages/4d/e8/98e06d3bc954e3c5b34e2a579ddf26255e762d21eb24fede458eff654c51/GitPython-2.1.11.tar.gz"
|
||||
sha256 "8237dc5bfd6f1366abeee5624111b9d6879393d84745a507de0fda86043b65a8"
|
||||
end
|
||||
|
||||
resource "idna" do
|
||||
url "https://files.pythonhosted.org/packages/65/c4/80f97e9c9628f3cac9b98bfca0402ede54e0563b56482e3e6e45c43c4935/idna-2.7.tar.gz"
|
||||
sha256 "684a38a6f903c1d71d6d5fac066b58d7768af4de2b832e426ec79c30daa94a16"
|
||||
url "https://files.pythonhosted.org/packages/ad/13/eb56951b6f7950cadb579ca166e448ba77f9d24efc03edd7e55fa57d04b7/idna-2.8.tar.gz"
|
||||
sha256 "c357b3f628cf53ae2c4c05627ecc484553142ca23264e593d327bcde5e9c3407"
|
||||
end
|
||||
|
||||
resource "jsonschema" do
|
||||
url "https://files.pythonhosted.org/packages/58/b9/171dbb07e18c6346090a37f03c7e74410a1a56123f847efed59af260a298/jsonschema-2.6.0.tar.gz"
|
||||
sha256 "6ff5f3180870836cae40f06fa10419f557208175f13ad7bc26caa77beb1f6e02"
|
||||
url "https://files.pythonhosted.org/packages/1f/7f/a020327823b9c405ee6f85ab3053ff171e10801b19cfe55c78bb0b3810e7/jsonschema-3.0.1.tar.gz"
|
||||
sha256 "0c0a81564f181de3212efa2d17de1910f8732fa1b71c42266d983cd74304e20d"
|
||||
end
|
||||
|
||||
resource "pyrsistent" do
|
||||
url "https://files.pythonhosted.org/packages/6c/ef/7781092174a42d0b57fb02a2eb23f78ebc8e588c9bd7455e1d1c7b1ea516/pyrsistent-0.15.3.tar.gz"
|
||||
sha256 "50cffebc87ca91b9d4be2dcc2e479272bcb466b5a0487b6c271f7ddea6917e14"
|
||||
end
|
||||
|
||||
resource "PyYAML" do
|
||||
url "https://files.pythonhosted.org/packages/9e/a3/1d13970c3f36777c583f136c136f804d70f500168edc1edea6daa7200769/PyYAML-3.13.tar.gz"
|
||||
sha256 "3ef3092145e9b70e3ddd2c7ad59bdd0252a94dfe3949721633e41344de00a6bf"
|
||||
url "https://files.pythonhosted.org/packages/a3/65/837fefac7475963d1eccf4aa684c23b95aa6c1d033a2c5965ccb11e22623/PyYAML-5.1.1.tar.gz"
|
||||
sha256 "b4bb4d3f5e232425e25dda21c070ce05168a786ac9eda43768ab7f3ac2770955"
|
||||
end
|
||||
|
||||
resource "ratelimiter" do
|
||||
|
|
@ -71,51 +88,32 @@ class Snakemake < Formula
|
|||
end
|
||||
|
||||
resource "requests" do
|
||||
url "https://files.pythonhosted.org/packages/54/1f/782a5734931ddf2e1494e4cd615a51ff98e1879cbe9eecbdfeaf09aa75e9/requests-2.19.1.tar.gz"
|
||||
sha256 "ec22d826a36ed72a7358ff3fe56cbd4ba69dd7a6718ffd450ff0e9df7a47ce6a"
|
||||
url "https://files.pythonhosted.org/packages/01/62/ddcf76d1d19885e8579acb1b1df26a852b03472c0e46d2b959a714c90608/requests-2.22.0.tar.gz"
|
||||
sha256 "11e007a8a2aa0323f5a921e9e6a2d7e4e67d9877e85773fba9ba6419025cbeb4"
|
||||
end
|
||||
|
||||
resource "six" do
|
||||
url "https://files.pythonhosted.org/packages/dd/bf/4138e7bfb757de47d1f4b6994648ec67a51efe58fa907c1e11e350cddfca/six-1.12.0.tar.gz"
|
||||
sha256 "d16a0141ec1a18405cd4ce8b4613101da75da0e9a7aec5bdd4fa804d0e0eba73"
|
||||
end
|
||||
|
||||
resource "smmap2" do
|
||||
url "https://files.pythonhosted.org/packages/3b/ba/e49102b3e8ffff644edded25394b2d22ebe3e645f3f6a8139129c4842ffe/smmap2-2.0.5.tar.gz"
|
||||
sha256 "29a9ffa0497e7f2be94ca0ed1ca1aa3cd4cf25a1f6b4f5f87f74b46ed91d609a"
|
||||
end
|
||||
|
||||
resource "urllib3" do
|
||||
url "https://files.pythonhosted.org/packages/3c/d2/dc5471622bd200db1cd9319e02e71bc655e9ea27b8e0ce65fc69de0dac15/urllib3-1.23.tar.gz"
|
||||
sha256 "a68ac5e15e76e7e5dd2b8f94007233e01effe3e50e8daddf69acfd81cb686baf"
|
||||
url "https://files.pythonhosted.org/packages/4c/13/2386233f7ee40aa8444b47f7463338f3cbdf00c316627558784e3f542f07/urllib3-1.25.3.tar.gz"
|
||||
sha256 "dbe59173209418ae49d485b87d1681aefa36252ee85884c31346debd19463232"
|
||||
end
|
||||
|
||||
resource "wrapt" do
|
||||
url "https://files.pythonhosted.org/packages/a0/47/66897906448185fcb77fc3c2b1bc20ed0ecca81a0f2f88eda3fc5a34fc3d/wrapt-1.10.11.tar.gz"
|
||||
sha256 "d4d560d479f2c21e1b5443bbd15fe7ec4b37fe7e53d335d3b9b0a7b1226fe3c6"
|
||||
url "https://files.pythonhosted.org/packages/23/84/323c2415280bc4fc880ac5050dddfb3c8062c2552b34c2e512eb4aa68f79/wrapt-1.11.2.tar.gz"
|
||||
sha256 "565a021fd19419476b9362b05eeaa094178de64f8361e44468f9e9d7843901e1"
|
||||
end
|
||||
|
||||
def install
|
||||
xy = Language::Python.major_minor_version "python3"
|
||||
|
||||
ENV.prepend_create_path "PYTHONPATH", buildpath/"cython/lib/python#{xy}/site-packages"
|
||||
|
||||
resource("Cython").stage do
|
||||
system "python3", *Language::Python.setup_install_args(buildpath/"cython")
|
||||
end
|
||||
|
||||
ENV.prepend_path "PATH", buildpath/"cython/bin"
|
||||
|
||||
resource("datrie").stage do
|
||||
system "./update_c.sh"
|
||||
ENV.delete "PYTHONPATH"
|
||||
ENV.prepend_create_path "PYTHONPATH", libexec/"vendor/lib/python#{xy}/site-packages"
|
||||
system "python3", *Language::Python.setup_install_args(libexec/"vendor")
|
||||
end
|
||||
|
||||
resources.each do |r|
|
||||
next if r.name == "datrie" || r.name == "Cython"
|
||||
|
||||
r.stage do
|
||||
system "python3", *Language::Python.setup_install_args(libexec/"vendor")
|
||||
end
|
||||
end
|
||||
|
||||
ENV.prepend_create_path "PYTHONPATH", libexec/"lib/python#{xy}/site-packages"
|
||||
system "python3", *Language::Python.setup_install_args(libexec)
|
||||
|
||||
bin.install Dir[libexec/"bin/*"]
|
||||
bin.env_script_all_files(libexec/"bin", :PYTHONPATH => ENV["PYTHONPATH"])
|
||||
virtualenv_install_with_resources
|
||||
end
|
||||
|
||||
test do
|
||||
|
|
@ -127,5 +125,6 @@ class Snakemake < Formula
|
|||
"touch {output}"
|
||||
EOS
|
||||
system "#{bin}/snakemake"
|
||||
assert_predicate testpath/"test.out", :exist?
|
||||
end
|
||||
end
|
||||
|
|
|
|||
Loading…
Reference in a new issue