aboutsummaryrefslogtreecommitdiff
path: root/gn/packages/cwl.scm
diff options
context:
space:
mode:
authorMuriithi Frederick Muriuki2018-12-14 16:22:08 +0300
committerMuriithi Frederick Muriuki2018-12-14 16:22:08 +0300
commit48670eaf1d59a6e52d8676bceb9f2cc996270228 (patch)
treebd486417687a3811e729ba6c4b9fc144ad16bf79 /gn/packages/cwl.scm
parent3825ddc719efb64c9194458b5d11a09156ded0c6 (diff)
parent9e84151973674af3cc31e0cbe5e6e1a9eeaa6ed4 (diff)
downloadguix-bioinformatics-48670eaf1d59a6e52d8676bceb9f2cc996270228.tar.gz
Merge branch 'master' of gitlab.com:genenetwork/guix-bioinformatics
Diffstat (limited to 'gn/packages/cwl.scm')
-rw-r--r--gn/packages/cwl.scm90
1 files changed, 62 insertions, 28 deletions
diff --git a/gn/packages/cwl.scm b/gn/packages/cwl.scm
index 4f04f41..5a01dbf 100644
--- a/gn/packages/cwl.scm
+++ b/gn/packages/cwl.scm
@@ -3,9 +3,14 @@
(define-module (gn packages cwl)
#:use-module ((guix licenses) #:prefix license:)
#:use-module (gnu packages)
+ #:use-module (gnu packages check)
#:use-module (gnu packages python)
#:use-module (gnu packages python-web)
+ #:use-module (gnu packages node)
#:use-module (gnu packages rdf)
+ #:use-module (gnu packages serialization)
+ #:use-module (gnu packages time)
+ #:use-module (gnu packages version-control)
#:use-module (gn packages python)
#:use-module (guix download)
#:use-module (guix packages)
@@ -16,55 +21,84 @@
; #:use-module (guix build-system trivial)
#:use-module (srfi srfi-1))
-(define-public python-cwltool ; guix: needs work
+(define-public cwltool ; guix: needs work
+ (let ((commit "e12d36b6efbc5d4a6ff7b4fbfd7387bff8f72727"))
(package
- (name "python-cwltool")
- (version "1.0.20150916041152")
+ (name "cwltool")
+ (version "1.0.20181012180214")
(source
(origin
- (method url-fetch)
- (uri (string-append
- "https://pypi.python.org/packages/source/c/cwltool/cwltool-"
- version
- ".tar.gz"))
+ ; (method url-fetch)
+ ; (uri (string-append
+ ; "https://pypi.python.org/packages/source/c/cwltool/cwltool-"
+ ; version
+ ; ".tar.gz"))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/genenetwork/cwltool.git")
+ (commit commit)))
+ (file-name (git-file-name name version))
(sha256
(base32
- "1kqxc6nvq4nr8qdv39ycdi6fhzaipgjpmbghsz94ij6jhf5r3dq2"))))
+ "1zhba1hfizrw3bxfmhpjds92pj79hyyv5k7sglw24z52kg1in67p"))))
(build-system python-build-system)
- (inputs
- `(("python-setuptools" ,python-setuptools)
+ (propagated-inputs ; a lot of these are used for testing
+ `(("git" ,git)
+ ("node" ,node)
+ ("python-bagit" ,python-bagit)
+ ("python-arcp" ,python-arcp)
+ ("python-setuptools" ,python-setuptools)
+ ("python-dateutil" ,python-dateutil)
+ ("python-pytest-cov" ,python-pytest-cov)
+ ("python-prov" ,python-prov)
+ ("python-pytest-runner" ,python-pytest-runner)
+ ("python-rdflib" ,python-rdflib)
("python-pyparsing" ,python-pyparsing)
- ))
- (propagated-inputs
- `(("python-schema-salad" ,python-schema-salad)
+ ("python-pytest-mock" ,python-pytest-mock)
+ ("python-mock" ,python-mock)
+ ("python-subprocess32" ,python-subprocess32)
+ ("python-ruamel.yaml" ,python-ruamel.yaml)
+ ("python-cachecontrol" ,python-cachecontrol)
+ ("python-lxml" ,python-lxml)
+ ("python-mypy-extensions" ,python-mypy-extensions)
+ ("python-mistune" ,python-mistune)
+ ("python-networkx" ,python-networkx)
+ ("python-schema-salad" ,python-schema-salad)
("python-html5lib" ,python-html5lib)
+ ("python-rdflib-jsonld" ,python-rdflib-jsonld)
+ ("python-typing-extensions" ,python-typing-extensions)
+ ("python-scandir" ,python-scandir)
+ ("python-psutil" ,python-psutil)
))
- (arguments `(#:tests? #f)) ;; CWL includes no tests.
+ ; (arguments `(#:tests? #f)) ;; CWL includes no tests.
+ (arguments
+ `(;#:phases
+ ; (modify-phases %standard-phases
+ ; (replace 'check
+ ; (lambda* (#:key inputs outputs #:allow-other-keys)
+ ; (invoke "python" "-m" "pytest")
+ ; )))
+ #:tests? #f)) ; Disable for now
+
(home-page
"https://github.com/common-workflow-language/common-workflow-language")
(synopsis
"Common workflow language reference implementation")
(description
"Common workflow language reference implementation")
- (license license:asl2.0)))
-
-(define-public python2-cwltool
- (package-with-python2 python-cwltool))
+ (license license:asl2.0))))
(define-public python-schema-salad
(package
(name "python-schema-salad")
- (version "1.0.2")
+ (version "3.0.20181129082112")
(source
(origin
(method url-fetch)
- (uri (string-append
- "https://pypi.python.org/packages/source/s/schema-salad/schema-salad-"
- version
- ".tar.gz"))
+ (uri (pypi-uri "schema-salad" version))
(sha256
(base32
- "09axiiirq73s1cs21n8mkdslaca2gxc2mlayyl6yiaq98cfgfh37"))))
+ "1xg70v82q053vz1sg8sc99alnkrm2kk05w6698vgmngl1767sk97"))))
(build-system python-build-system)
(arguments `(#:tests? #f)) ;; CWL includes no tests.
(inputs
@@ -73,7 +107,7 @@
("python-rdflib-jsonld" ,python-rdflib-jsonld)
("python-mistune" ,python-mistune)))
(propagated-inputs
- `(("python-rdflib-4.2" ,python-rdflib-4.2)
+ `(("python-rdflib" ,python-rdflib)
("python-avro" ,python-avro)
("python-pyyaml" ,python-pyyaml)
("python-requests" ,python-requests)
@@ -87,5 +121,5 @@
"Schema Annotations for Linked Avro Data (SALAD)")
(license license:asl2.0)))
-(define-public python2-schema-salad
- (package-with-python2 python-schema-salad))
+; (define-public python2-schema-salad
+; (package-with-python2 python-schema-salad))