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authorPjotr Prins2018-01-30 11:15:27 +0000
committerPjotr Prins2018-01-30 11:15:27 +0000
commit7da6542cdbece8787ef2ae0b42f25ea24b54b174 (patch)
tree281d14cfc096eaab4f9ceb3f0e1d88518420e952 /gn/packages
parentdb13b8db8dd09ee1c4d022383070785549290dee (diff)
parentf4e392ce9252e67304b74289fef0568ac1d66ac6 (diff)
downloadguix-bioinformatics-7da6542cdbece8787ef2ae0b42f25ea24b54b174.tar.gz
Merge branch 'master' of gitlab.com:genenetwork/guix-bioinformatics
Diffstat (limited to 'gn/packages')
-rw-r--r--gn/packages/genenetwork.scm2
-rw-r--r--gn/packages/javascript.scm6
-rw-r--r--gn/packages/python.scm38
-rw-r--r--gn/packages/sambamba.scm2
4 files changed, 41 insertions, 7 deletions
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm
index 3139599..cf58b8e 100644
--- a/gn/packages/genenetwork.scm
+++ b/gn/packages/genenetwork.scm
@@ -182,7 +182,9 @@ location of a putative QTL.")
"0ji929xgzypyhchcfy9xa1sz04w322ibs2khc8s3qiddxjqdglrz"))))
(propagated-inputs `( ;; propagated for development purposes
("python" ,python-2) ;; probably superfluous
+ ("coreutils" ,coreutils)
("git" ,git)
+ ("vim" ,vim)
("which" ,which)
("grep" ,grep)
("r" ,r)
diff --git a/gn/packages/javascript.scm b/gn/packages/javascript.scm
index 74509d6..7fc82af 100644
--- a/gn/packages/javascript.scm
+++ b/gn/packages/javascript.scm
@@ -10,10 +10,10 @@
#:use-module (srfi srfi-1))
(define-public javascript-twitter-post-fetcher
- (let ((commit "12d1693980ef836af4d5eee74a0aec5c65b8e6c3"))
+ (let ((commit "27440ffebd4c1ba7abc9aec92a581155715f2e4e"))
(package
(name "javascript-twitter-post-fetcher")
- (version (string-append "17.0.2" "-" (string-take commit 7)))
+ (version (string-append "17.0.3" "-" (string-take commit 7)))
(source (origin
(method git-fetch)
(uri (git-reference
@@ -22,7 +22,7 @@
(file-name (string-append name "-" commit))
(sha256
(base32
- "1afs5dd3mbih016vganvm9bcmn3cg3cvwh34hhk5n04qvb2aphdm"))))
+ "159z8izf510086d8sa79k4mml6sw1gycb1r1r9ri1kyw2k9knmqa"))))
(build-system trivial-build-system)
(native-inputs `(("source" ,source)))
(arguments
diff --git a/gn/packages/python.scm b/gn/packages/python.scm
index d489b7a..848cf8d 100644
--- a/gn/packages/python.scm
+++ b/gn/packages/python.scm
@@ -112,8 +112,34 @@ functions.")
(license license:expat))
)
+(define-public python-inotify ; guix candidate
+(package
+ (name "python-inotify")
+ (version "0.2.9")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "inotify" version))
+ (sha256
+ (base32
+ "043sbm9q8ca4fhn19knwpsxgzfgm5ik75m0bl7dp9hjy6p3v3zzn"))))
+ (build-system python-build-system)
+ (propagated-inputs
+ `(("inotify-tools" ,inotify-tools)))
+ (arguments `(#:tests? #f)) ;; No tests.
+ (home-page "https://pypi.python.org/pypi/inotify")
+ (synopsis
+ "Python inotify.")
+ (description
+ "Python inotify.")
+ (license license:gpl2))
+)
+
+(define-public python2-inotify
+ (package-with-python2 python-inotify))
+
+
(define-public gunicorn ; guix candidate
- ; python-plotly, python-requests, python-pytz
(package
(name "gunicorn")
(version "19.7.1")
@@ -125,7 +151,13 @@ functions.")
(base32
"08mnl5l1p47q5wk38d7mafnhsqk50yba0l9kvc2vwrx61jgidqgf"))))
(build-system python-build-system)
- (arguments `(#:tests? #f)) ;; No tests.
+ ; (inputs
+ ; `(("python2-inotify" ,python2-inotify)))
+ (propagated-inputs
+ `(("inotify-tools" ,inotify-tools)))
+ (arguments `(
+ #:python ,python-2 ; GN2 is still python2
+ #:tests? #f)) ;; No tests.
(home-page "http://gunicorn.org")
(synopsis
".")
@@ -134,7 +166,7 @@ functions.")
(license license:expat))
)
-(define-public python2-flask-sqlalchemy
+(define-public python2-flask-sqlalchemy
(package-with-python2 python-flask-sqlalchemy))
(define-public python-xlsxwriter ; guix ready
diff --git a/gn/packages/sambamba.scm b/gn/packages/sambamba.scm
index c2759fa..ee6a973 100644
--- a/gn/packages/sambamba.scm
+++ b/gn/packages/sambamba.scm
@@ -92,7 +92,7 @@
;; The current build compiles htslib statically into the
;; executable. On top of that, we need to patch the latest
;; version of htslib to have it working with Sambamba.
- (and
+ (and
(copy-recursively (assoc-ref inputs "htslib-src") "htslib")
(copy-recursively (assoc-ref inputs "dlang-undeaD-src") "undeaD")
(copy-recursively (assoc-ref inputs "biod-src") "BioD"))))