diff options
Diffstat (limited to 'gn/packages/genenetwork.scm')
| -rw-r--r-- | gn/packages/genenetwork.scm | 29 |
1 files changed, 21 insertions, 8 deletions
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 671d5e9..8a76327 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -31,13 +31,13 @@ #: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) #:use-module (gn packages crates-io) #:use-module (gn packages elixir) #:use-module (gn packages gemma) - #:use-module (gn packages graphviz) #:use-module (gn packages javascript) #:use-module (gn packages phewas) #:use-module (gn packages python) @@ -259,8 +259,8 @@ implemented, light on server resource usage, and fairly speedy.") (("rust-rand" ,rust-rand-0.6) ("rust-structopt" ,rust-structopt-0.2) ("rust-rayon" ,rust-rayon-1) - ("rust-serde" ,rust-serde-1.0) - ("rust-serde-json" ,rust-serde-json-1.0) + ("rust-serde" ,rust-serde-1) + ("rust-serde-json" ,rust-serde-json-1) ("rust-ndarray" ,rust-ndarray-0.12)) #:phases (modify-phases %standard-phases @@ -318,6 +318,7 @@ implemented, light on server resource usage, and fairly speedy.") ("rust-qtlreaper" ,rust-qtlreaper) ("nginx" ,nginx) ("python-twint" ,python-twint) + ("python2-coverage" ,python2-coverage) ("python2-flask" ,python2-flask) ("python2-gunicorn-gn" ,python2-gunicorn-gn) ; ("python2-pillow" ,python2-pillow) - for later! @@ -334,7 +335,9 @@ implemented, light on server resource usage, and fairly speedy.") ("python2-scipy" ,python2-scipy) ("python2-lxml" ,python2-lxml) ("python2-mechanize" ,python2-mechanize) + ("python2-mock" ,python2-mock) ("python2-mysqlclient" ,python2-mysqlclient) + ("python2-nose" ,python-nose2) ("python2-numarray" ,python2-numarray) ("python2-numpy" ,python2-numpy) ("python2-pandas" ,python2-pandas) @@ -823,8 +826,8 @@ 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)) @@ -836,12 +839,11 @@ written in C") (file-name (git-file-name name version)) (sha256 (base32 - "1s735dj8kf98gf5w58p10zzyc5766gn27j4j5yh07ksadg7h1kdi")))) + "0xmmmjyvh80yd8b0cjrwpdmxl8k9zj5ly65r2g9aygx74njsp4fi")))) (build-system gnu-build-system) - (propagated-inputs + (native-inputs `(("ghostscript" ,ghostscript) ("graphviz" ,graphviz-2.26) - ("httpd" ,httpd22-mod-python-24) ("python24" ,python-2.4) ("python-piddle" ,python24-piddle) ("wget" ,wget))) @@ -879,6 +881,17 @@ written in C") (("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") |