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

1 files changed, 50 insertions, 11 deletions

diff --git a/gn/packages/cwl.scm b/gn/packages/cwl.scm
index 5a01dbf..245af84 100644
--- a/gn/packages/cwl.scm
+++ b/gn/packages/cwl.scm
@@ -4,6 +4,7 @@
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (gnu packages)
   #:use-module (gnu packages check)
+  #:use-module (gnu packages databases)
   #:use-module (gnu packages python)
   #:use-module (gnu packages python-web)
   #:use-module (gnu packages node)
@@ -22,7 +23,7 @@
   #:use-module (srfi srfi-1))
 
 (define-public cwltool ; guix: needs work
-  (let ((commit "e12d36b6efbc5d4a6ff7b4fbfd7387bff8f72727"))
+  (let ((commit "15539fba76993f951af9eba913bea6d677c74005"))
   (package
     (name "cwltool")
     (version "1.0.20181012180214")
@@ -35,12 +36,12 @@
         ;       ".tar.gz"))
          (method git-fetch)
          (uri (git-reference
-               (url "https://github.com/genenetwork/cwltool.git")
+               (url "https://github.com/genenetwork/cwltool.git") ;; my repo for Python 3.7
                (commit commit)))
-         (file-name (git-file-name name version))
+         (file-name (git-file-name name (string-append version "-" (string-take commit 7))))
         (sha256
           (base32
-            "1zhba1hfizrw3bxfmhpjds92pj79hyyv5k7sglw24z52kg1in67p"))))
+            "1qwfa82car7477sy0cb5bj4964w7zq7dcw2bdcls6c2i9qdp0586"))))
     (build-system python-build-system)
     (propagated-inputs ; a lot of these are used for testing
      `(("git" ,git)
@@ -66,7 +67,6 @@
        ("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)
        ))
@@ -88,17 +88,56 @@
       "Common workflow language reference implementation")
     (license license:asl2.0))))
 
+(define-public python-cachecontrol
+  (package
+    (name "python-cachecontrol")
+    (version "0.11.7")
+    (source
+     (origin
+       (method url-fetch)
+       ;; Pypi does not have tests.
+       (uri (string-append
+             "https://github.com/ionrock/cachecontrol/archive/v"
+             version ".tar.gz"))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32
+         "1yfhwihx1b1xjsx0r19va2m0r2s91im03x4d7pwzp87368f2lkkp"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:tests? #f)) ;; Recent version breaks on cherrypy
+    (native-inputs
+     `(("python-pytest" ,python-pytest)
+       ("python-redis" ,python-redis)
+       ("python-webtest" ,python-webtest)
+       ("python-mock" ,python-mock)))
+    (propagated-inputs
+     `(("python-requests" ,python-requests)
+       ("python-lockfile" ,python-lockfile)))
+    (home-page "https://github.com/ionrock/cachecontrol")
+    (synopsis "The httplib2 caching algorithms for use with requests")
+    (description "CacheControl is a port of the caching algorithms in
+@code{httplib2} for use with @code{requests} session objects.")
+    (license license:asl2.0)))
+
+
 (define-public python-schema-salad
+  (let ((commit "eb85c3d49b99b7643e8a12248e2dc05504910c1e"))
   (package
     (name "python-schema-salad")
     (version "3.0.20181129082112")
     (source
       (origin
-        (method url-fetch)
-        (uri (pypi-uri "schema-salad" version))
-        (sha256
-          (base32
-            "1xg70v82q053vz1sg8sc99alnkrm2kk05w6698vgmngl1767sk97"))))
+        ; (method url-fetch)
+        ; (uri (pypi-uri "schema-salad" version))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/genenetwork/schema_salad.git") ;; my repo for Python3.7
+             (commit commit)))
+       (file-name (git-file-name name (string-append version "-" (string-take commit 7))))
+       (sha256
+        (base32
+         "174f224zzjr0nbjlq3ypciyfijnibasysrgjswvx8yhan2dizlhr"))))
     (build-system python-build-system)
     (arguments `(#:tests? #f)) ;; CWL includes no tests.
     (inputs
@@ -119,7 +158,7 @@
       "Schema Annotations for Linked Avro Data (SALAD)")
     (description
       "Schema Annotations for Linked Avro Data (SALAD)")
-    (license license:asl2.0)))
+    (license license:asl2.0))))
 
 ; (define-public python2-schema-salad
 ;  (package-with-python2 python-schema-salad))