diff options
Diffstat (limited to 'gn/packages/genecup.scm')
| -rw-r--r-- | gn/packages/genecup.scm | 31 |
1 files changed, 16 insertions, 15 deletions
diff --git a/gn/packages/genecup.scm b/gn/packages/genecup.scm index 0cd776f..d761826 100644 --- a/gn/packages/genecup.scm +++ b/gn/packages/genecup.scm @@ -7,7 +7,9 @@ #:use-module (guix git-download) #:use-module (guix build-system python) #:use-module (gnu packages admin) + #:use-module (gnu packages base) #:use-module (gnu packages bioinformatics) + #:use-module (gnu packages compression) #:use-module (gnu packages javascript) #:use-module (gnu packages machine-learning) #:use-module (gnu packages python) @@ -18,7 +20,8 @@ #:use-module (gn packages javascript) #:use-module (gn packages machine-learning) #:use-module (gn packages python) - #:use-module (gn packages web)) + #:use-module (gn packages web) + #:use-module (gn packages machine-learning)) (define use-corrected-inputs (package-input-rewriting/spec @@ -27,19 +30,6 @@ `(("tensorflow" . ,(const tensorflow-native)) ("python-h5py" . ,(const python-h5py-2))))) -(define-public python-keras-no-tests - (hidden-package - (package - (inherit python-keras) - (source - (origin - (inherit (package-source python-keras)))) - (arguments - (substitute-keyword-arguments (package-arguments python-keras) - ((#:phases phases) - `(modify-phases ,phases - (delete 'check)))))))) - (define-public hrdp-project (package @@ -153,6 +143,11 @@ if __name__ == '__main__': (lambda _ (substitute* "server.py" (("4200") "4204")))) + ;; TODO: This should be disabled in the source. + (add-after 'unpack 'disable-debug-mode + (lambda _ + (substitute* "server.py" + (("debug=True") "debug=False")))) (add-after 'unpack 'make-files-writable (lambda _ (for-each make-file-writable (find-files ".")))) @@ -179,6 +174,10 @@ if __name__ == '__main__': (("https.*1.12.9/umd/popper.min.js.*\\\">") "/static/popper.min.js\">")) (substitute* "ratspub.py" (("hostname") (string-append inetutils "/bin/hostname")))))) + (add-after 'unpack 'extract-pubmed-archive + (lambda _ + (invoke "gzip" "-d" "minipubmed.tgz") + (invoke "tar" "xvf" "minipubmed.tar"))) (replace 'install (lambda* (#:key outputs #:allow-other-keys) (let ((out (assoc-ref outputs "out"))) @@ -230,6 +229,8 @@ if __name__ == '__main__': (inputs `(("edirect" ,edirect) ("inetutils" ,inetutils) + ("gzip" ,gzip) + ("tar" ,tar) ("python-bcrypt" ,python-bcrypt) ("python-flask-sqlalchemy" ,python-flask-sqlalchemy) ("python-keras" ,python-keras-no-tests) @@ -263,7 +264,7 @@ concepts and a list of keywords for each concept.") (version "HEAD-of-master-branch") (source (git-checkout - (url "https://github.com/hakangunturkun/GeneCup") + (url "https://git.genenetwork.org/genecup") (branch "master"))))) (define-public genecup-with-tensorflow-native |