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

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"))))