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02/02: gnu: Add python-cgatcore.
From: |
guix-commits |
Subject: |
02/02: gnu: Add python-cgatcore. |
Date: |
Mon, 14 Jun 2021 17:15:47 -0400 (EDT) |
rekado pushed a commit to branch master
in repository guix.
commit 748d3a2b8aabe63965bd71392e5e7bdd2ed1b6b0
Author: Ricardo Wurmus <rekado@elephly.net>
AuthorDate: Mon Jun 14 23:13:06 2021 +0200
gnu: Add python-cgatcore.
* gnu/packages/bioinformatics.scm (python-cgatcore): New variable.
---
gnu/packages/bioinformatics.scm | 59 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 59 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index d09f55e..7a1c8cc 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -60,6 +60,7 @@
#: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 @@
#: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 @@
#: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 @@ usually ignored by other methods or only used for
filtering.")
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