diff options
| -rw-r--r-- | gn/packages/genenetwork.scm | 23 |
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") |