Merge branch 'master' of gitlab.com:genenetwork/guix-bioinformatics

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))