mirror of
https://git.savannah.gnu.org/git/guix.git
synced 2025-01-18 21:46:35 +01:00
gnu: Add python-bed-reader.
* gnu/packages/bioinformatics.scm (python-bed-reader): New variable. Change-Id: Iad3f1d1c05abe706d8cd52a4d046247a5a9738e2
This commit is contained in:
Ricardo Wurmus
parent
251c7a2049
commit
1091274ee0
1 changed files with 120 additions and 0 deletions
|
|
@ -85,6 +85,7 @@ (define-module (gnu packages bioinformatics)
|
|||
#:use-module (gnu packages cran)
|
||||
#:use-module (gnu packages crates-compression)
|
||||
#:use-module (gnu packages crates-io)
|
||||
#:use-module (gnu packages crates-web)
|
||||
#:use-module (gnu packages curl)
|
||||
#:use-module (gnu packages docbook)
|
||||
#:use-module (gnu packages documentation)
|
||||
|
|
@ -2047,6 +2048,125 @@ (define-public python-bcbio-gff/biopython-1.73
|
|||
(modify-inputs (package-propagated-inputs python-bcbio-gff)
|
||||
(replace "python-biopython" python-biopython-1.73))))))
|
||||
|
||||
(define-public python-bed-reader
|
||||
(package
|
||||
(name "python-bed-reader")
|
||||
(version "1.0.6")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (pypi-uri "bed_reader" version))
|
||||
(sha256
|
||||
(base32 "1c8ibwvz3b069w7ffh9aasz16lfkmx4z0249c2v909a21mrkkd6n"))))
|
||||
(build-system cargo-build-system)
|
||||
(arguments
|
||||
(list
|
||||
;; Many of the tests (both the Rust tests and the Python tests) require
|
||||
;; Internet access to fetch samples.
|
||||
#:tests? #false
|
||||
#:install-source? #false
|
||||
#:features '(list "extension-module")
|
||||
#:cargo-test-flags '(list "--features=extension-module")
|
||||
#:cargo-inputs
|
||||
`(("rust-anyinput" ,rust-anyinput-0.1)
|
||||
("rust-bytecount" ,rust-bytecount-0.6)
|
||||
("rust-byteorder" ,rust-byteorder-1)
|
||||
("rust-bytes" ,rust-bytes-1)
|
||||
("rust-cloud-file" ,rust-cloud-file-0.2)
|
||||
("rust-derive-builder" ,rust-derive-builder-0.20)
|
||||
("rust-dpc-pariter" ,rust-dpc-pariter-0.4)
|
||||
("rust-fetch-data" ,rust-fetch-data-0.2)
|
||||
("rust-futures-util" ,rust-futures-util-0.3)
|
||||
("rust-itertools" ,rust-itertools-0.13)
|
||||
("rust-ndarray" ,rust-ndarray-0.16)
|
||||
("rust-ndarray-npy" ,rust-ndarray-npy-0.9)
|
||||
("rust-num-traits" ,rust-num-traits-0.2)
|
||||
("rust-numpy" ,rust-numpy-0.22)
|
||||
("rust-pyo3" ,rust-pyo3-0.22)
|
||||
("rust-pyo3-build-config" ,rust-pyo3-build-config-0.22)
|
||||
("rust-rayon" ,rust-rayon-1)
|
||||
("rust-statrs" ,rust-statrs-0.17)
|
||||
("rust-thiserror" ,rust-thiserror-1)
|
||||
("rust-tokio" ,rust-tokio-1))
|
||||
#:cargo-development-inputs
|
||||
`(("rust-anyhow" ,rust-anyhow-1)
|
||||
("rust-ndarray-rand" ,rust-ndarray-rand-0.15)
|
||||
("rust-rusoto-credential" ,rust-rusoto-credential-0.48)
|
||||
("rust-temp-testdir" ,rust-temp-testdir-0.2)
|
||||
("rust-thousands" ,rust-thousands-0.2))
|
||||
#:imported-modules
|
||||
(append %cargo-build-system-modules
|
||||
%pyproject-build-system-modules)
|
||||
#:modules
|
||||
'((guix build cargo-build-system)
|
||||
((guix build pyproject-build-system) #:prefix py:)
|
||||
(guix build utils))
|
||||
#:phases
|
||||
#~(modify-phases %standard-phases
|
||||
(add-after 'install 'prepare-python-module
|
||||
(lambda _
|
||||
;; We don't use maturin.
|
||||
(delete-file "pyproject.toml")
|
||||
(call-with-output-file "pyproject.toml"
|
||||
(lambda (port)
|
||||
(format port "\
|
||||
[build-system]
|
||||
build-backend = 'setuptools.build_meta'
|
||||
requires = ['setuptools']
|
||||
")))
|
||||
(call-with-output-file "setup.cfg"
|
||||
(lambda (port)
|
||||
(format port "\
|
||||
[metadata]
|
||||
name = bed-reader
|
||||
version = ~a
|
||||
|
||||
[options]
|
||||
packages = find:
|
||||
|
||||
[options.packages.find]
|
||||
exclude =
|
||||
src
|
||||
docs
|
||||
tests
|
||||
Cargo.toml
|
||||
" #$version)))))
|
||||
(add-after 'prepare-python-module 'enable-bytecode-determinism
|
||||
(assoc-ref py:%standard-phases 'enable-bytecode-determinism))
|
||||
(add-after 'enable-bytecode-determinism 'build-python-module
|
||||
(assoc-ref py:%standard-phases 'build))
|
||||
(add-after 'build-python-module 'install-python-module
|
||||
(assoc-ref py:%standard-phases 'install))
|
||||
(add-after 'install-python-module 'install-python-library
|
||||
(lambda _
|
||||
(let ((site (string-append #$output "/lib/python"
|
||||
#$(version-major+minor
|
||||
(package-version python))
|
||||
"/site-packages")))
|
||||
(mkdir-p site)
|
||||
(copy-file "target/release/libbed_reader.so"
|
||||
(string-append site "/bed_reader/bed_reader.so")))))
|
||||
(add-after 'install-python-library 'add-install-to-pythonpath
|
||||
(assoc-ref py:%standard-phases 'add-install-to-pythonpath))
|
||||
(add-after 'add-install-to-pythonpath 'check-python
|
||||
(lambda* (#:key tests? test-flags #:allow-other-keys)
|
||||
(when tests?
|
||||
(apply invoke "pytest" "-v" #$output test-flags)))))))
|
||||
(native-inputs (list python-pytest
|
||||
python-pytest-cov
|
||||
python-pytest-datadir
|
||||
python-pytest-doctestplus
|
||||
python-recommonmark
|
||||
python-sphinx))
|
||||
(inputs (list python-wrapper))
|
||||
(propagated-inputs (list python-numpy python-pandas python-pooch))
|
||||
(home-page "https://fastlmm.github.io/")
|
||||
(synopsis "Read and write the PLINK BED format, simply and efficiently")
|
||||
(description
|
||||
"This package lets you read and write the PLINK BED format, simply and
|
||||
efficiently.")
|
||||
(license license:asl2.0)))
|
||||
|
||||
;; Note: the name on PyPi is "biofluff".
|
||||
(define-public python-biofluff
|
||||
(package
|
||||
|
|
|
|||
Loading…
Reference in a new issue