diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 59 |
1 files changed, 59 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index d09f55e5b8..7a1c8cc8e3 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 |