Moving genenetwork stuff into its own module

2 files changed, 200 insertions, 151 deletions

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 896767b..43e61a2 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -47,45 +47,6 @@
   #:use-module (gn packages statistics)
   #:use-module (srfi srfi-1))
 
-(define-public my-deploy
-  (package
-    (name "my-deploy")
-    (version "0.0.1")
-    (source #f)
-    (build-system trivial-build-system)
-    (arguments
-     `(#:guile ,%bootstrap-guile
-       #:modules ((guix build utils))
-       #:builder
-       (let* ((out  (assoc-ref %outputs "out"))
-              (bash (assoc-ref %build-inputs "bash"))
-              (foo  (string-append out "/foo")))
-         (begin
-           (use-modules (guix build utils))
-           (mkdir out)
-           (call-with-output-file foo
-             (lambda (p)
-               (format p
-                       "#!~a~%echo \"${GUIX_FOO} ${GUIX_BAR}\"~%"
-                       bash)))
-           (chmod foo #o777)
-           ;; wrap-program uses `which' to find bash for the wrapper
-           ;; shebang, but it can't know about the bootstrap bash in
-           ;; the store, since it's not named "bash".  Help it out a
-           ;; bit by providing a symlink it this package's output.
-           (symlink bash (string-append out "/bash"))
-           (setenv "PATH" out)
-           (wrap-program foo `("GUIX_FOO" prefix ("hello")))
-           (wrap-program foo `("GUIX_BAR" prefix ("world")))
-           #t))))
-    (inputs `(("bash" ,(search-bootstrap-binary "bash"
-                                                (%current-system)))))
-
-    (home-page #f)
-    (synopsis #f)
-    (description #f)
-    (license #f)))
-
 (define-public r-wgcna
 (package
   (name "r-wgcna")
@@ -307,118 +268,6 @@ association studies (GWAS).")
     (license license:gpl3))))
 
 
-(define-public genenetwork1
-  (let ((commit "d622c803b"))
-  (package
-    (name "genenetwork1")
-    (version (string-append "1.0-" commit ))
-    (source (origin
-             (method git-fetch)
-             (uri (git-reference
-                   (url "https://github.com/genenetwork/genenetwork.git")
-                   ;; (url "https://github.com/pjotrp/genenetwork.git")
-                   (commit commit)))
-             (file-name (string-append name "-" commit)) 
-             (sha256
-              (base32
-               "14fzfcm4vl20mlhxjslfa01i1nmxpk8lbxmfvpq6dyfc22ir62py"))))
-    (propagated-inputs `(
-              ("python" ,python-2) ;; probably superfluous
-              ("r" ,r) 
-    ))
-    (inputs `(
-              ;; http://spring211.uthsc.edu/gn/thirdparty.tbz
-              ;; graphviz-2.22.2  htmlgen  json  numarray-1.5.2  piddle  PIL  pp-1.5.7  pyx  pyXLWriter  svg
-              ("mysql" ,mysql)
-              ("nginx" ,nginx)
-              ("graphviz" ,graphviz)
-              ; ("python2-jinja2" ,python2-jinja2)
-              ; ("python2-sqlalchemy" ,python2-sqlalchemy)
-              ; ("python2-setuptools" ,python2-setuptools)
-              ; ("python2-scipy" ,python2-scipy)
-              ;; looks like python-numarray is not needed
-              ; ("python2-numpy" ,python2-numpy)
-              ; ("python2-pandas" ,python2-pandas)
-              ; ("python2-passlib" ,python2-passlib)
-              ; ("python2-redis" ,python2-redis)
-              ; ("python2-requests" ,python2-requests)
-              ; ("python2-simplejson" ,python2-simplejson)
-              ; ("python2-pyyaml" ,python2-pyyaml)
-              ;; python-yolk is not needed
-              ("python2-pil" ,python2-pil)
-              ("python2-numarray" ,python2-numarray)
-              ("plink" ,plink) ;; gn1
-              ; ("r-qtl" ,r-qtl)
-              ))
-    (build-system python-build-system)
-    (arguments
-     `(#:python ,python-2
-       #:tests? #f))   ; no 'setup.py test'
-    (home-page "http://genenetwork.org/")
-    (synopsis "Full genenetwork services")
-    (description "Genenetwork installation sumo.")
-    (license license:agpl3+))))
-
-(define-public genenetwork2
-  (let ((commit "9e9475053"))
-  (package
-    (name "genenetwork2")
-    (version (string-append "2.0-" commit ))
-    (source (origin
-             (method git-fetch)
-             (uri (git-reference
-                   ;; (url "https://github.com/genenetwork/genenetwork2.git")
-                   (url "https://github.com/pjotrp/genenetwork2.git")
-                   (commit commit)))
-             (file-name (string-append name "-" commit)) 
-             (sha256
-              (base32
-               "09hvy9mf4dnmkb8qg49viffzrxk53m2kr4r955m84dxaa5pdrjhd"))))
-    (propagated-inputs `(  ;; propagated for development purposes
-              ("python" ,python-2) ;; probably superfluous
-              ("r" ,r)
-              ("redis" ,redis)
-              ("mysql" ,mysql)
-              ("gemma" ,gemma-git)
-              ("pylmm-gn2" ,pylmm-gn2)
-              ("plink2" ,plink-ng)
-              ("nginx" ,nginx)
-              ("python2-flask" ,python2-flask)
-              ("python2-htmlgen-gn" ,python2-htmlgen-gn)
-              ("python2-jinja2" ,python2-jinja2)
-              ("python2-sqlalchemy" ,python2-sqlalchemy)
-              ("python2-flask-sqlalchemy" ,python2-flask-sqlalchemy)
-              ("python2-setuptools" ,python2-setuptools)
-              ("python2-scipy" ,python2-scipy)
-              ;; looks like python-numarray is not needed
-              ("python2-mysqlclient" ,python2-mysqlclient)
-              ("python2-numarray" ,python2-numarray)
-              ("python2-numpy" ,python2-numpy)
-              ("python2-pandas" ,python2-pandas)
-              ("python2-parallel" ,python2-parallel)
-              ("python2-passlib" ,python2-passlib)
-              ("python2-piddle" ,python2-piddle)
-              ("python2-redis" ,python2-redis)
-              ("python2-requests" ,python2-requests)
-              ("python2-rpy2" ,python2-rpy2)
-              ("python2-scipy" ,python2-scipy)
-              ("python2-simplejson" ,python2-simplejson)
-              ("python2-pyyaml" ,python2-pyyaml)
-              ("python2-xlsxwriter" ,python2-xlsxwriter)
-              ;; python-yolk is not needed
-              ("plink" ,plink) 
-              ("qtlreaper" ,qtlreaper) 
-              ("r-qtl" ,r-qtl)
-              ))
-    (build-system python-build-system)
-    (arguments
-     `(#:python ,python-2
-       #:tests? #f))   ; no 'setup.py test'
-    (home-page "http://genenetwork.org/")
-    (synopsis "Full genenetwork services")
-    (description "Genenetwork installation sumo.")
-    (license license:agpl3+))))
-
 (define-public rdmd
   (package
     (name "rdmd")
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm
new file mode 100644
index 0000000..b2e7f00
--- /dev/null
+++ b/gn/packages/genenetwork.scm
@@ -0,0 +1,200 @@
+;; Bioinformatics module
+
+(define-module (gn packages genenetwork)
+  #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (guix packages)
+  #:use-module (guix utils)
+  #:use-module (guix download)
+  #:use-module (guix git-download)
+  #:use-module (guix build-system gnu)
+  #:use-module (guix build-system cmake)
+  #:use-module (guix build-system perl)
+  #:use-module (guix build-system python)
+  ;; #:use-module (guix build-system ruby)
+  #:use-module (guix build-system r)
+  #:use-module (guix build-system trivial)
+  #:use-module (gnu packages)
+  #:use-module (gnu packages algebra)
+  #:use-module (gnu packages base)
+  #:use-module (gnu packages bioinformatics)
+  #:use-module (gnu packages boost)
+  #:use-module (gnu packages compression)
+  #:use-module (gnu packages databases)
+  #:use-module (gnu packages cpio)
+  #:use-module (gnu packages file)
+  #:use-module (gnu packages gcc)
+  #:use-module (gnu packages graphviz)
+  #:use-module (gnu packages java)
+  #:use-module (gnu packages linux)
+  #:use-module (gnu packages ldc)
+  #:use-module (gnu packages machine-learning)
+  #:use-module (gnu packages maths)
+  #:use-module (gnu packages ncurses)
+  #:use-module (gnu packages perl)
+  #:use-module (gnu packages pkg-config)
+  #:use-module (gnu packages popt)
+  #:use-module (gnu packages protobuf)
+  #:use-module (gnu packages python)
+  #:use-module (gnu packages statistics)
+  #:use-module (gnu packages tbb)
+  #:use-module (gnu packages textutils)
+  #:use-module (gnu packages vim)
+  #:use-module (gnu packages web)
+  #:use-module (gnu packages xml)
+  #:use-module (gnu packages zip)
+  #:use-module (gnu packages bootstrap)
+  #:use-module (gn packages python)
+  #:use-module (gn packages statistics)
+  #:use-module (srfi srfi-1))
+
+(define-public my-deploy
+  (package
+    (name "my-deploy")
+    (version "0.0.1")
+    (source #f)
+    (build-system trivial-build-system)
+    (arguments
+     `(#:guile ,%bootstrap-guile
+       #:modules ((guix build utils))
+       #:builder
+       (let* ((out  (assoc-ref %outputs "out"))
+              (bash (assoc-ref %build-inputs "bash"))
+              (foo  (string-append out "/foo")))
+         (begin
+           (use-modules (guix build utils))
+           (mkdir out)
+           (call-with-output-file foo
+             (lambda (p)
+               (format p
+                       "#!~a~%echo \"${GUIX_FOO} ${GUIX_BAR}\"~%"
+                       bash)))
+           (chmod foo #o777)
+           ;; wrap-program uses `which' to find bash for the wrapper
+           ;; shebang, but it can't know about the bootstrap bash in
+           ;; the store, since it's not named "bash".  Help it out a
+           ;; bit by providing a symlink it this package's output.
+           (symlink bash (string-append out "/bash"))
+           (setenv "PATH" out)
+           (wrap-program foo `("GUIX_FOO" prefix ("hello")))
+           (wrap-program foo `("GUIX_BAR" prefix ("world")))
+           #t))))
+    (inputs `(("bash" ,(search-bootstrap-binary "bash"
+                                                (%current-system)))))
+
+    (home-page #f)
+    (synopsis #f)
+    (description #f)
+    (license #f)))
+
+
+(define-public genenetwork1
+  (let ((commit "d622c803b"))
+  (package
+    (name "genenetwork1")
+    (version (string-append "1.0-" commit ))
+    (source (origin
+             (method git-fetch)
+             (uri (git-reference
+                   (url "https://github.com/genenetwork/genenetwork.git")
+                   ;; (url "https://github.com/pjotrp/genenetwork.git")
+                   (commit commit)))
+             (file-name (string-append name "-" commit)) 
+             (sha256
+              (base32
+               "14fzfcm4vl20mlhxjslfa01i1nmxpk8lbxmfvpq6dyfc22ir62py"))))
+    (propagated-inputs `(
+              ("python" ,python-2) ;; probably superfluous
+              ("r" ,r) 
+    ))
+    (inputs `(
+              ;; http://spring211.uthsc.edu/gn/thirdparty.tbz
+              ;; graphviz-2.22.2  htmlgen  json  numarray-1.5.2  piddle  PIL  pp-1.5.7  pyx  pyXLWriter  svg
+              ("mysql" ,mysql)
+              ("nginx" ,nginx)
+              ("graphviz" ,graphviz)
+              ; ("python2-jinja2" ,python2-jinja2)
+              ; ("python2-sqlalchemy" ,python2-sqlalchemy)
+              ; ("python2-setuptools" ,python2-setuptools)
+              ; ("python2-scipy" ,python2-scipy)
+              ;; looks like python-numarray is not needed
+              ; ("python2-numpy" ,python2-numpy)
+              ; ("python2-pandas" ,python2-pandas)
+              ; ("python2-passlib" ,python2-passlib)
+              ; ("python2-redis" ,python2-redis)
+              ; ("python2-requests" ,python2-requests)
+              ; ("python2-simplejson" ,python2-simplejson)
+              ; ("python2-pyyaml" ,python2-pyyaml)
+              ;; python-yolk is not needed
+              ("python2-pil" ,python2-pil)
+              ("python2-numarray" ,python2-numarray)
+              ("plink" ,plink) ;; gn1
+              ; ("r-qtl" ,r-qtl)
+              ))
+    (build-system python-build-system)
+    (arguments
+     `(#:python ,python-2
+       #:tests? #f))   ; no 'setup.py test'
+    (home-page "http://genenetwork.org/")
+    (synopsis "Full genenetwork services")
+    (description "Genenetwork installation sumo.")
+    (license license:agpl3+))))
+
+(define-public genenetwork2
+  (let ((commit "9e9475053"))
+  (package
+    (name "genenetwork2")
+    (version (string-append "2.0-" commit ))
+    (source (origin
+             (method git-fetch)
+             (uri (git-reference
+                   ;; (url "https://github.com/genenetwork/genenetwork2.git")
+                   (url "https://github.com/pjotrp/genenetwork2.git")
+                   (commit commit)))
+             (file-name (string-append name "-" commit)) 
+             (sha256
+              (base32
+               "09hvy9mf4dnmkb8qg49viffzrxk53m2kr4r955m84dxaa5pdrjhd"))))
+    (propagated-inputs `(  ;; propagated for development purposes
+              ("python" ,python-2) ;; probably superfluous
+              ("r" ,r)
+              ("redis" ,redis)
+              ("mysql" ,mysql)
+              ("gemma" ,gemma-git)
+              ("pylmm-gn2" ,pylmm-gn2)
+              ("plink2" ,plink-ng)
+              ("nginx" ,nginx)
+              ("python2-flask" ,python2-flask)
+              ("python2-htmlgen-gn" ,python2-htmlgen-gn)
+              ("python2-jinja2" ,python2-jinja2)
+              ("python2-sqlalchemy" ,python2-sqlalchemy)
+              ("python2-flask-sqlalchemy" ,python2-flask-sqlalchemy)
+              ("python2-setuptools" ,python2-setuptools)
+              ("python2-scipy" ,python2-scipy)
+              ;; looks like python-numarray is not needed
+              ("python2-mysqlclient" ,python2-mysqlclient)
+              ("python2-numarray" ,python2-numarray)
+              ("python2-numpy" ,python2-numpy)
+              ("python2-pandas" ,python2-pandas)
+              ("python2-parallel" ,python2-parallel)
+              ("python2-passlib" ,python2-passlib)
+              ("python2-piddle" ,python2-piddle)
+              ("python2-redis" ,python2-redis)
+              ("python2-requests" ,python2-requests)
+              ("python2-rpy2" ,python2-rpy2)
+              ("python2-scipy" ,python2-scipy)
+              ("python2-simplejson" ,python2-simplejson)
+              ("python2-pyyaml" ,python2-pyyaml)
+              ("python2-xlsxwriter" ,python2-xlsxwriter)
+              ;; python-yolk is not needed
+              ("plink" ,plink) 
+              ("qtlreaper" ,qtlreaper) 
+              ("r-qtl" ,r-qtl)
+              ))
+    (build-system python-build-system)
+    (arguments
+     `(#:python ,python-2
+       #:tests? #f))   ; no 'setup.py test'
+    (home-page "http://genenetwork.org/")
+    (synopsis "Full genenetwork services")
+    (description "Genenetwork installation sumo.")
+    (license license:agpl3+))))