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-rw-r--r--gn/packages/genenetwork.scm23
1 files changed, 16 insertions, 7 deletions
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm
index 4654ccd..7925bd5 100644
--- a/gn/packages/genenetwork.scm
+++ b/gn/packages/genenetwork.scm
@@ -679,8 +679,8 @@ written in C")
(license license:agpl3+))))
(define-public genenetwork1
- (let ((commit "19791ce6b3c38be8cbf9bc9cd3e95dbee14116c2") ; Aug 23, 2018
- (revision "1"))
+ (let ((commit "acf65ac9ae4be395c07c1629758f7408bf4eab5f") ; June 3, 2020
+ (revision "2"))
(package
(name "genenetwork1")
(version (git-version "0.0.0" revision commit))
@@ -692,7 +692,7 @@ written in C")
(file-name (git-file-name name version))
(sha256
(base32
- "1s735dj8kf98gf5w58p10zzyc5766gn27j4j5yh07ksadg7h1kdi"))))
+ "0xmmmjyvh80yd8b0cjrwpdmxl8k9zj5ly65r2g9aygx74njsp4fi"))))
(build-system gnu-build-system)
(native-inputs
`(("ghostscript" ,ghostscript)
@@ -707,9 +707,8 @@ written in C")
(delete 'configure)
(delete 'build)
(add-after 'patch-generated-file-shebangs 'patch-more-files
- (lambda* (#:key inputs outputs #:allow-other-keys)
- (let ((piddle (assoc-ref inputs "python-piddle"))
- (out (assoc-ref outputs "out")))
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let ((piddle (assoc-ref inputs "python-piddle")))
(substitute* "web/webqtl/networkGraph/networkGraphUtils.py"
(("/usr/local/bin/neato") (which "neato"))
(("/usr/local/bin/circo") (which "circo"))
@@ -730,12 +729,22 @@ written in C")
(("/usr/bin/python") (which "python"))
(("/usr/bin/env python") (which "python")))
(substitute* "web/webqtl/base/webqtlConfigLocal.py"
- (("/gnshare/gn") out)
(("PythonPath.*")
(string-append "PythonPath = '" (which "python") "'\n"))
(("PIDDLE_FONT_PATH.*/lib")
(string-append "PIDDLE_FONT_PATH = '" piddle "/lib"))))
#t))
+ (add-after 'patch-generated-file-shebangs 'changes-for-deployed-service
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((out (assoc-ref outputs "out")))
+ (substitute* "web/webqtl/base/webqtlConfigLocal.py"
+ ;; Where GN1 is located:
+ (("/gnshare/gn") out)
+ ;; Where the database is located:
+ (("tux01") "localhost"))
+ ;; This directory is expected to be writable
+ (symlink "/tmp" "web/tmp")
+ #t)))
(add-before 'install 'replace-htaccess-file
(lambda _
(delete-file "web/webqtl/.htaccess")