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authorMuriithi Frederick Muriuki2019-02-18 14:43:59 +0300
committerMuriithi Frederick Muriuki2019-02-18 14:43:59 +0300
commitf5ffd9d54da0ca3634326c8652077aaa9605fd61 (patch)
tree35f2bed63fa24a4d8136691a5d3352e565731bbc /gn
parent70658e4b52819cb2c5ceb189d98b2e3bbda26d4f (diff)
parent7a5ba50f1df5473bf43abeae34648ee39698a6b1 (diff)
downloadguix-bioinformatics-f5ffd9d54da0ca3634326c8652077aaa9605fd61.tar.gz
Merge branch 'master' of gitlab.com:genenetwork/guix-bioinformatics
Diffstat (limited to 'gn')
-rw-r--r--gn/packages/cwl.scm61
-rw-r--r--gn/packages/edash.scm37
-rw-r--r--gn/packages/python.scm8
3 files changed, 88 insertions, 18 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))
diff --git a/gn/packages/edash.scm b/gn/packages/edash.scm
index 6324d3a..8d23a08 100644
--- a/gn/packages/edash.scm
+++ b/gn/packages/edash.scm
@@ -5,14 +5,17 @@
#:use-module (guix build-system trivial)
#:use-module (guix build-system python)
#:use-module (gnu packages web)
+ #:use-module (gnu packages base)
#:use-module (gnu packages python)
#:use-module (gnu packages python-web)
+ #:use-module (gnu packages python-xyz)
#:use-module (gnu packages python-crypto)
#:use-module (gnu packages compression)
#:use-module (gnu packages time)
#:use-module (gnu packages databases)
#:use-module (gnu packages check)
#:use-module (gn packages web)
+ #:use-module (gnu packages sqlite)
#:use-module (gn packages python))
(define-public python-s3transfer-0.1.13
@@ -442,6 +445,30 @@ with the Specification.")
"Connexion - API first applications with OpenAPI/Swagger and Flask")
(license license:asl2.0)))
+(define-public python-flask-cors
+ (package
+ (name "python-flask-cors")
+ (version "3.0.7")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "Flask-Cors" version))
+ (sha256
+ (base32
+ "1v6gq4vjgyxi8q8lxawpdfhq01adb4bznnabp08ks5nzbwibz43y"))))
+ (build-system python-build-system)
+ (inputs
+ `(("python-flask" ,python-flask)
+ ("python-six" ,python-six)
+ ("python-nose" ,python-nose)))
+ (home-page
+ "https://github.com/corydolphin/flask-cors")
+ (synopsis
+ "A Flask extension adding a decorator for CORS support")
+ (description
+ "A Flask extension adding a decorator for CORS support")
+ (license license:expat)))
+
(define-public edash
(let ((md5 "93e745e9c"))
(package
@@ -460,6 +487,7 @@ with the Specification.")
;;(inputs `(("sassc" ,sassc)))
(propagated-inputs
`(("python" ,python)
+ ("glibc-locales" ,glibc-locales)
("gunicorn" ,gunicorn)
("python-wrapper" ,python-wrapper)
("python-elasticsearch" ,python-elasticsearch)
@@ -467,7 +495,7 @@ with the Specification.")
("python-jinja2" ,python-jinja2)
("python-markdown" ,python-markdown)
("python-misaka" ,python-misaka)
- ("python-pygit2" ,python-pygit2)
+ ;; ("python-pygit2" ,python-pygit2)
("web-bootstrap" ,web-bootstrap)
;;("sassc" ,sassc)
("python-boto3" ,python-boto3)
@@ -480,8 +508,11 @@ with the Specification.")
("python-flask-mail" ,python-flask-mail)
("python-flask-wtf" ,python-flask-wtf)
("sqlite" ,sqlite)
- ("python-ipython" ,python-ipython)
- ))
+ ;; ("python-ipython" ,python-ipython)
+ ("python-swagger-ui-bundle" ,python-swagger-ui-bundle)
+ ("python-connexion" ,python-connexion)
+ ("python-schedule" ,python-schedule)
+ ("python-flask-cors" ,python-flask-cors)))
(arguments
`(#:modules ((guix build utils))
#:builder
diff --git a/gn/packages/python.scm b/gn/packages/python.scm
index 75f7cab..651a635 100644
--- a/gn/packages/python.scm
+++ b/gn/packages/python.scm
@@ -37,6 +37,7 @@
#:use-module (gnu packages web)
#:use-module (gnu packages xml)
#:use-module (gnu packages xorg)
+ #:use-module (gnu packages python-xyz)
#:use-module (guix packages)
#:use-module (guix download)
#:use-module (guix git-download)
@@ -379,7 +380,7 @@ functions.")
(define-public python-setuptools
(package
(name "python-setuptools")
- (version "40.6.2")
+ (version "40.6.0")
(source
(origin
(method url-fetch)
@@ -753,9 +754,8 @@ the older versions.")
(base32
"04h8brrbbx151dfa2cvvlnxgmb5wa00mhd2z7nd20s8kyibfkq1p"))))
(build-system python-build-system)
- (propagated-inputs
- `(("python-version" ,python-version)
- ("python-typing" ,python-typing)))
+ (inputs
+ `(("python-version" ,python-version)))
(home-page "http://www.mypy-lang.org/")
(synopsis
"Experimental type system extensions for programs checked with the mypy typechecker.")