From df5f7651f94891effdcef4ec67af5a04c888713e Mon Sep 17 00:00:00 2001
From: pjotrp
Date: Sat, 13 Feb 2016 12:25:30 +0100
Subject: GN2: adding packages

---
 gn/packages/bioinformatics.scm |  3 ++
 gn/packages/python.scm         | 97 ++++++++++++++++++++++++++++++++++++++++++
 gn/packages/slurm.scm          |  6 +--
 3 files changed, 103 insertions(+), 3 deletions(-)

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index c576127..c796708 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -232,11 +232,13 @@ confidence region for the location of a putative QTL.")
     (inputs `(
               ("mysql" ,mysql)
               ("nginx" ,nginx)
+              ("python2-flask" ,python2-flask)
               ("python2-jinja2" ,python2-jinja2)
               ("python2-sqlalchemy" ,python2-sqlalchemy)
               ("python2-setuptools" ,python2-setuptools)
               ("python2-scipy" ,python2-scipy)
               ;; looks like python-numarray is not needed
+              ("python2-mysqlclient" ,python2-mysqlclient)
               ("python2-numpy" ,python2-numpy)
               ("python2-pandas" ,python2-pandas)
               ("python2-passlib" ,python2-passlib)
@@ -244,6 +246,7 @@ confidence region for the location of a putative QTL.")
               ("python2-requests" ,python2-requests)
               ("python2-simplejson" ,python2-simplejson)
               ("python2-pyyaml" ,python2-pyyaml)
+              ("python-xlsxwriter" ,python-xlsxwriter)
               ;; python-yolk is not needed
               ("plink" ,plink) 
               ("r-qtl" ,r-qtl)
diff --git a/gn/packages/python.scm b/gn/packages/python.scm
index 8f53d54..41d6ee1 100644
--- a/gn/packages/python.scm
+++ b/gn/packages/python.scm
@@ -8,6 +8,7 @@
   #:use-module (gnu packages gcc)
   #:use-module (gnu packages ghostscript)
   #:use-module (gnu packages glib)
+  #:use-module (gnu packages gnupg)
   #:use-module (gnu packages gtk)
   #:use-module (gnu packages icu4c)
   #:use-module (gnu packages image)
@@ -41,6 +42,68 @@
   #:use-module (guix build-system trivial)
   #:use-module (srfi srfi-1))
 
+(define-public python-flask
+(package
+  (name "python-flask")
+  (version "0.10.1")
+  (source
+    (origin
+      (method url-fetch)
+      (uri (pypi-uri "Flask" version))
+      (sha256
+        (base32
+          "0wrkavjdjndknhp8ya8j850jq7a1cli4g5a93mg8nh1xz2gq50sc"))))
+  (build-system python-build-system)
+  (inputs
+   `(("python-setuptools" ,python-setuptools)
+     ; ("python-itsdangerous" ,python-itsdangerous)
+     ; ("python-jinja2" ,python-jinja2)
+     ; ("python-werkzeug" ,python-werkzeug)
+     ))
+  (propagated-inputs
+   `(
+     ("python-itsdangerous" ,python-itsdangerous)
+     ("python-jinja2" ,python-jinja2)
+     ("python-werkzeug" ,python-werkzeug)
+     ))
+  
+  (arguments
+   `(#:tests? #f)) ; No tests
+  (home-page "http://github.com/mitsuhiko/flask/")
+  (synopsis
+    "A microframework based on Werkzeug, Jinja2 and good intentions")
+  (description
+    "A microframework based on Werkzeug, Jinja2 and good intentions")
+  (license license:bsd-3)))
+
+(define-public python2-flask
+  (package-with-python2 python-flask))
+
+(define-public python-xlsxwriter
+(package
+  (name "python-xlsxwriter")
+  (version "0.8.4")
+  (source
+    (origin
+      (method url-fetch)
+      (uri (pypi-uri "XlsxWriter" version))
+      (sha256
+        (base32
+          "0hv6bknnj9mlvvkdnlzycs0s97vrakmyh91ddb7ynjaqp8gl434z"))))
+  (build-system python-build-system)
+  (inputs
+    `(("python-setuptools" ,python-setuptools)))
+  (home-page
+    "https://github.com/jmcnamara/XlsxWriter")
+  (synopsis
+    "A Python module for creating Excel XLSX files.")
+  (description
+    "A Python module for creating Excel XLSX files.")
+  (license license:bsd-3)))
+
+(define-public python2-xlsxwriter
+  (package-with-python2 python-xlsxwriter))
+
 (define-public python-rdflib-jsonld
   (package
     (name "python-rdflib-jsonld")
@@ -176,6 +239,40 @@ powerful language for representing information.")
 (define-public python2-shellescape
   (package-with-python2 python-shellescape))
 
+(define-public python-mysqlclient
+(package
+  (name "python-mysqlclient")
+  (version "1.3.7")
+  (source
+    (origin
+      (method url-fetch)
+      (uri (pypi-uri "mysqlclient" version))
+      (sha256
+        (base32
+          "06qzgwk7j66k8ggx51i6wxx0f0zsppp7w4bh6gjd0cr9rfs86jn7"))))
+  (build-system python-build-system)
+  (inputs
+   `(
+     ("mysql" ,mysql)
+     ("python-nose" ,python-nose)
+     ("zlib" ,zlib)
+     ("openssl" ,openssl)
+     ("libgcrypt" ,libgcrypt)
+     ))
+  (propagated-inputs
+   `(("python-setuptools" ,python-setuptools)
+     ))
+  (arguments
+   `(#:tests? #f))   ; wants a running MySQL server
+  (home-page
+    "https://github.com/PyMySQL/mysqlclient-python")
+  (synopsis "Python interface to MySQL")
+  (description "Python interface to MySQL")
+  (license license:gpl3)))
+
+(define-public python2-mysqlclient
+  (package-with-python2 python-mysqlclient))
+
 (define-public python2-numarray
   (package
     (name "python2-numarray")
diff --git a/gn/packages/slurm.scm b/gn/packages/slurm.scm
index 8f7ac1a..9e3d063 100644
--- a/gn/packages/slurm.scm
+++ b/gn/packages/slurm.scm
@@ -37,9 +37,9 @@
 
 (define-public slurm-llnl
   (package
-    (name "slurm-llnl")
-    (version "15-08-6-1")
-    (source (origin
+   (name "slurm-llnl")
+   (version "15-08-6-1")
+   (source (origin
              (method url-fetch)
              (uri (string-append "https://github.com/SchedMD/slurm/archive/slurm-"
                                  version ".tar.gz"))
-- 
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