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authorPjotr Prins2020-11-21 04:33:15 -0600
committerPjotr Prins2020-11-21 04:33:36 -0600
commitf129c4fc90fd70b6a468537bda8c497f2bee2277 (patch)
treea0044ecd93be38efa331e3ae813c15c6ec7d3e17
parentad741c19d6a7bfc16610fa25689398243deaa7a5 (diff)
downloadguix-bioinformatics-f129c4fc90fd70b6a468537bda8c497f2bee2277.tar.gz
cwltools: updated
-rw-r--r--gn/packages/cwl.scm66
-rw-r--r--gn/packages/python.scm10
2 files changed, 55 insertions, 21 deletions
diff --git a/gn/packages/cwl.scm b/gn/packages/cwl.scm
index 3e0576c..9871ed9 100644
--- a/gn/packages/cwl.scm
+++ b/gn/packages/cwl.scm
@@ -2,29 +2,61 @@
#:use-module ((guix licenses) #:prefix license:)
#:use-module (gn packages python)
#:use-module (guix download)
+ #:use-module (guix git-download)
#:use-module (guix packages)
#:use-module (guix build-system python)
#:use-module (gnu packages)
#:use-module (gnu packages check)
+ #:use-module (gnu packages graphviz)
#:use-module (gnu packages python-web)
#:use-module (gnu packages python-xyz)
#: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 (gnu packages xml))
-(define-public cwltool
+(define-public python-pydot ;; can be updated in GNU Guix - this is a copy
(package
- (name "cwltool")
- (version "3.0.20200710214758")
+ (name "python-pydot")
+ (version "1.4.1")
(source
- (origin
- (method url-fetch)
- (uri (pypi-uri "cwltool" version))
- (sha256
- (base32
- "1qbqkhinkhzg98jf24d5gnafsw23kng76rbi2hfvzl18bdsp1zz5"))))
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "pydot" version))
+ (sha256
+ (base32
+ "00az4cbf8bv447lkk9xi6pjm7gcc7ia33y4pm71fwfwis56rv76l"))))
+ (build-system python-build-system)
+ (native-inputs
+ ;; For tests.
+ `(("python-chardet" ,python-chardet)))
+ (propagated-inputs
+ `(("python-pyparsing" ,python-pyparsing)))
+ (home-page "https://github.com/erocarrera/pydot")
+ (synopsis "Python interface to Graphviz's DOT language")
+ (description
+ "Pydot provides an interface to create, handle, modify and process
+graphs in Graphviz's DOT language, written in pure Python.")
+ (license license:expat)))
+
+
+(define-public cwltool
+ (let ((commit "78fe9d41ee5a44f8725dfbd7028e4a5ee42949cf")
+ (revision "1"))
+ (package
+ (name "cwltool")
+ (version "3.0.20201117141248")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/common-workflow-language/cwltool.git")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1awf99n7aglxc5zszrlrv6jxp355jp45ws7wpsgjlgcdv7advn0w"))))
(build-system python-build-system)
(arguments
`(#:phases
@@ -38,9 +70,7 @@
(lambda _
;; Tries to connect to the internet.
(delete-file "tests/test_udocker.py")
- (substitute* "tests/test_http_input.py"
- (("https://raw.githubusercontent.com/common-workflow-language/cwltool/main")
- "."))
+ (delete-file "tests/test_http_input.py")
(substitute* "tests/test_load_tool.py"
(("def test_load_graph_fragment_from_packed")
"@pytest.mark.skip(reason=\"Disabled by Guix\")\ndef test_load_graph_fragment_from_packed"))
@@ -53,10 +83,13 @@
"@pytest.mark.skip(reason=\"Disabled by Guix\")\ndef test_v1_0_arg_empty_prefix_separate_false"))
#t)))))
(propagated-inputs
- `(("python-bagit" ,python-bagit)
+ `(("git" ,git)
+ ("python-argcomplete" ,python-argcomplete)
+ ("python-bagit" ,python-bagit)
("python-coloredlogs" ,python-coloredlogs)
("python-mypy-extensions" ,python-mypy-extensions)
("python-prov" ,python-prov)
+ ("python-pydot" ,python-pydot)
("python-psutil" ,python-psutil)
("python-rdflib" ,python-rdflib)
("python-requests" ,python-requests)
@@ -85,7 +118,7 @@
(synopsis "Common workflow language reference implementation")
(description
"Common workflow language reference implementation.")
- (license license:asl2.0)))
+ (license license:asl2.0))))
(define-public cwl-runner
(package
@@ -105,5 +138,6 @@
"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)))
+ "Common workflow language alternate entry point to allow cwl-runner
+script as an implementation-agnostic script interpreter.")
+ (license license:asl2.0)))
diff --git a/gn/packages/python.scm b/gn/packages/python.scm
index 00194e1..a9c2770 100644
--- a/gn/packages/python.scm
+++ b/gn/packages/python.scm
@@ -1100,14 +1100,14 @@ server.")
(define-public python-schema-salad
(package
(name "python-schema-salad")
- (version "7.0.20200612160654")
+ (version "7.0.20200811075006")
(source
(origin
(method url-fetch)
(uri (pypi-uri "schema-salad" version))
(sha256
(base32
- "15ma3lb6fkfc6sj75hnmmg0jj8q3pc5yrlyx15lpdd4dcp2jc39s"))))
+ "0wanbwmqb189x1m0vacnhpivfsr8rwbqknngivzxxs8j46yj80bg"))))
(build-system python-build-system)
(propagated-inputs
`(("python-cachecontrol" ,python-cachecontrol-0.11)
@@ -1116,8 +1116,8 @@ server.")
("python-rdflib" ,python-rdflib)
("python-rdflib-jsonld" ,python-rdflib-jsonld)
("python-requests" ,python-requests)
- ;; This needs to be fixed before upstreaming
- ("python-ruamel.yaml" ,python38-ruaml.yaml-0.15.76)
+ ;; This needs to be fixed before upstreaming - fixed?
+ ("python-ruamel.yaml" ,python-ruamel.yaml)
("python-setuptools" ,python-setuptools)
("python-typing-extensions" ,python-typing-extensions)))
(native-inputs
@@ -1528,7 +1528,7 @@ handles recursion and lists.")
(description "This package provides a SPARQL Slurper for rdflib.")
(license license:asl2.0)))
-(define-public python38-ruaml.yaml-0.15.76
+(define-public python38-ruaml.yaml-0.15.76 ;; no longer in use
(package
(inherit python-ruamel.yaml)
(name "python-ruamel.yaml")