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authorEfraim Flashner2020-09-23 05:26:21 -0500
committerEfraim Flashner2020-09-23 05:26:21 -0500
commit79fafeea964e97645cd1e98ddbb77a73a5f3ac62 (patch)
tree3b4d67238b0461c4112c0ab808126de006034f65
parent25197c3bbec7919d7a6c2f3baa87826d5ee4fd32 (diff)
downloadguix-bioinformatics-79fafeea964e97645cd1e98ddbb77a73a5f3ac62.tar.gz
genenetwork1: Update package and service
-rw-r--r--gn/packages/genenetwork.scm36
-rw-r--r--gn/services/genenetwork.scm7
2 files changed, 26 insertions, 17 deletions
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm
index c730666..369b1ab 100644
--- a/gn/packages/genenetwork.scm
+++ b/gn/packages/genenetwork.scm
@@ -21,6 +21,7 @@
#:use-module (gnu packages compression)
#:use-module (gnu packages databases)
#:use-module (gnu packages ghostscript)
+ #:use-module (gnu packages graphviz)
#:use-module (gnu packages python)
#:use-module (gnu packages python-check)
#:use-module (gnu packages python-crypto)
@@ -35,7 +36,6 @@
#:use-module (gnu packages web)
#:use-module (gnu packages wget)
#:use-module (gnu packages xml)
- #:use-module (past packages graphviz)
#:use-module (past packages python)
#:use-module (gn packages bioinformatics)
#:use-module (gn packages twint)
@@ -740,7 +740,7 @@ written in C")
(build-system gnu-build-system)
(native-inputs
`(("ghostscript" ,ghostscript)
- ("graphviz" ,graphviz-2.26)
+ ("graphviz" ,graphviz)
("python24" ,python-2.4)
("python-piddle" ,python24-piddle)
("wget" ,wget)))
@@ -770,8 +770,7 @@ written in C")
(substitute* '("web/webqtl/maintainance/addRif.py"
"web/webqtl/networkGraph/networkGraphPage.py"
"web/webqtl/utility/svg.py")
- (("/usr/bin/python") (which "python"))
- (("/usr/bin/env python") (which "python")))
+ (("/usr/bin/(env )?python") (which "python")))
(substitute* "web/webqtl/base/webqtlConfigLocal.py"
(("PythonPath.*")
(string-append "PythonPath = '" (which "python") "'\n"))
@@ -782,23 +781,34 @@ written in C")
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
(substitute* "web/webqtl/base/webqtlConfigLocal.py"
- ;; Where GN1 is located:
+ ;; Where GN1 is located: (GNROOT)
(("/gnshare/gn") out)
- ;; Where the database is located:
+ ;; Where the database is located: (sql_host)
(("tux01") "localhost"))
- ;(("tux01.uthsc.edu") "lily.uthsc.edu"))
- ;; This directory is expected to be writable.
+ (substitute* '("web/webqtl/maintainance/QTL_Reaper_cal_lrs.py")
+ (("128\\.169\\.5\\.59") "localhost"))
+ ;; This directory (TMPDIR) is expected to be writable by apache.
;; /tmp is private inside the container.
(symlink "/tmp" "web/tmp")
- ;; We mount the genotypes folder in the OS-config and
- ;; provide the symlink to that point in the package.
+ ;; IMGDIR is expected to be writable.
+ (symlink "/tmp" "web/image")
+ (system "chmod 0777 web/tmp")
+ ;; More writable locations:
+ (substitute* (list "web/webqtl/collection/ExportSelectionDetailInfoPage.py"
+ "web/webqtl/pairScan/DirectPlotPage.py"
+ "web/webqtl/updateTrait/DataUpdatePage.py"
+ "web/webqtl/utility/Plot.py")
+ (("/gnshare/gn/web/debug_file.txt") "/tmp/debug_file.txt"))
+ ;; We mount the genotypes folder (GENODIR) in the OS-config and
+ ;; provide the symlink to that location from the package.
;; And now the directory is magically available!
(symlink "/gnshare/gn/web/genotypes" "web/genotypes")
+ (substitute* "web/webqtl/base/webqtlConfig.py"
+ (("http://www.genenetwork.org") "http://gn1-test.genenetwork.org"))
#t)))
(add-after 'unpack 'use-local-links
(lambda _
(substitute* '("web/javascript/menu_items.js"
- "web/webqtl/base/webqtlConfig.py"
"web/webqtl/maintainance/updateMenuJS.py")
(("http://(www|gn1).genenetwork.org") ""))
@@ -823,10 +833,6 @@ written in C")
(find-files "web/dbdoc" "\\.html"))
(("src=\\\"http://www.genenetwork.org") "src=\""))
#t))
- (add-before 'install 'replace-htaccess-file
- (lambda _
- (delete-file "web/webqtl/.htaccess")
- #t))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(copy-recursively "." (assoc-ref outputs "out"))
diff --git a/gn/services/genenetwork.scm b/gn/services/genenetwork.scm
index d72590d..74723ca 100644
--- a/gn/services/genenetwork.scm
+++ b/gn/services/genenetwork.scm
@@ -88,13 +88,16 @@
python24-svg-GN1
%base-packages))
- (services (list (service httpd-service-type
+ (services (list (service special-files-service-type
+ ;; The genotypes folder doesn't have it's shebangs patched.
+ `(("/usr/bin/python" ,(file-append python-2.4 "/bin/python"))))
+ (service httpd-service-type
(httpd-configuration
;; Must be a httpd-2.2 variant.
(package httpd22-with-mod-python)
(config
(httpd-config-file
- (server-name "www.genenetwork.org")
+ (server-name "gn1-test.genenetwork.org")
;; Defaults to httpd, should be same as 'package' above.
(server-root httpd22-with-mod-python)
(user "nobody")