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gnu: Add python-cgatcore.

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* gnu/packages/bioinformatics.scm (python-cgatcore): New variable.
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Ricardo Wurmus 2021-06-14 23:13:06 +02:00
parent b63cae13c1
commit 748d3a2b8a
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59
gnu/packages/bioinformatics.scm
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@ -60,6 +60,7 @@ (define-module (gnu packages bioinformatics)
#:use-module (guix build-system trivial)
#:use-module (guix deprecation)
#:use-module (gnu packages)
#:use-module (gnu packages admin)
#:use-module (gnu packages assembly)
#:use-module (gnu packages autotools)
#:use-module (gnu packages algebra)
@ -106,6 +107,7 @@ (define-module (gnu packages bioinformatics)
#:use-module (gnu packages linux)
#:use-module (gnu packages lisp-xyz)
#:use-module (gnu packages logging)
#:use-module (gnu packages lsof)
#:use-module (gnu packages machine-learning)
#:use-module (gnu packages man)
#:use-module (gnu packages maths)
@ -125,6 +127,7 @@ (define-module (gnu packages bioinformatics)
#:use-module (gnu packages python-build)
#:use-module (gnu packages python-check)
#:use-module (gnu packages python-compression)
#:use-module (gnu packages python-crypto)
#:use-module (gnu packages python-science)
#:use-module (gnu packages python-web)
#:use-module (gnu packages python-xyz)
@ -14177,6 +14180,62 @@ (define-public python-pyliftover
coordinates between different assemblies.")
(license license:expat)))
(define-public python-cgatcore
(package
(name "python-cgatcore")
(version "0.6.7")
;; The version of pypi does not include test data.
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/cgat-developers/cgat-core")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"17vk88v1bx7x02ibzkc9i7ir4b5p1hcjr38jpsfzyzxr68352d5k"))))
(build-system python-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'fix-references
(lambda _
(substitute* "cgatcore/pipeline/execution.py"
(("#!/bin/bash") (string-append "#!" (which "bash")))
(("executable=\"/bin/bash\"")
(string-append "executable=\"" (which "bash") "\""))
(("\\\\time") (which "time")))))
(delete 'check)
(add-after 'install 'check
(lambda* (#:key tests? inputs outputs #:allow-other-keys)
(when tests?
(add-installed-pythonpath inputs outputs)
;; Requires network access
(delete-file "tests/test_pipeline_execution.py")
(invoke "python" "-m" "pytest" "-v")))))))
(native-inputs
`(("python-pytest" ,python-pytest)
("lsof" ,lsof)
("hostname" ,inetutils)
("openssl" ,openssl)))
(inputs
`(("time" ,time)))
(propagated-inputs
`(("python-apsw" ,python-apsw)
("python-gevent" ,python-gevent)
("python-pandas" ,python-pandas)
("python-paramiko" ,python-paramiko)
("python-pyyaml" ,python-pyyaml)
("python-ruffus" ,python-ruffus)
("python-sqlalchemy" ,python-sqlalchemy)))
(home-page "https://github.com/cgat-developers/cgat-core")
(synopsis "Computational genomics analysis toolkit")
(description
"CGAT-core is a set of libraries and helper functions used to enable
researchers to design and build computational workflows for the analysis of
large-scale data-analysis.")
(license license:expat)))
(define-public ensembl-vep
(let* ((api-version "103")
(api-module