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authorpjotrp2018-12-14 04:38:50 +0000
committerpjotrp2018-12-14 04:38:50 +0000
commit2372ecc00bb08b033bba48316edd17ef9a6e974b (patch)
tree91679c21f0bf75329bdfe2d0dc6e165b03a00b82 /gn/packages
parent792c615b32c8eef93a8da7993b1cda32b3e3a0b8 (diff)
downloadguix-bioinformatics-2372ecc00bb08b033bba48316edd17ef9a6e974b.tar.gz
CWL final packages - tests pass in principle (except for some networking)
Diffstat (limited to 'gn/packages')
-rw-r--r--gn/packages/cwl.scm29
-rw-r--r--gn/packages/python.scm21
2 files changed, 42 insertions, 8 deletions
diff --git a/gn/packages/cwl.scm b/gn/packages/cwl.scm
index 2642f90..785a6ed 100644
--- a/gn/packages/cwl.scm
+++ b/gn/packages/cwl.scm
@@ -6,8 +6,11 @@
#: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)
@@ -33,23 +36,33 @@
(base32
"0pk0jlac2vl6vfihdq07agzz9dasw84yjz5ladcbwnmzzl022cg7"))))
(build-system python-build-system)
- (inputs
- `(("python-bagit" ,python-bagit)
+ (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-typing-extensions" ,python-typing-extensions)
("python-pyparsing" ,python-pyparsing)
+ ("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)
- ))
- (propagated-inputs
- `(("python-schema-salad" ,python-schema-salad)
+ ("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
@@ -102,5 +115,5 @@
"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))
diff --git a/gn/packages/python.scm b/gn/packages/python.scm
index 808eb9d..75f7cab 100644
--- a/gn/packages/python.scm
+++ b/gn/packages/python.scm
@@ -763,3 +763,24 @@ the older versions.")
"Experimental type system extensions for programs checked with the mypy typechecker.")
(license #f))
)
+
+
+(define-public python-arcp
+(package
+ (name "python-arcp")
+ (version "0.2.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "arcp" version))
+ (sha256
+ (base32
+ "0h8sn0mlb6vb8wqqnqc4pxdklrkyx3p72afdhm7b9kyalrqzd7dd"))))
+ (build-system python-build-system)
+ (home-page "http://arcp.readthedocs.io/")
+ (synopsis
+ "arcp (Archive and Package) URI parser and generator")
+ (description
+ "arcp (Archive and Package) URI parser and generator")
+ (license license:asl2.0))
+)