diff options
| -rw-r--r-- | gn/packages/genenetwork.scm | 82 |
1 files changed, 37 insertions, 45 deletions
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 9401374..d3c4993 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -446,11 +446,20 @@ implemented, light on server resource usage, and fairly speedy.") (license license:agpl3+)))) (define-public python3-genenetwork2 - (let ((commit "1538ffd33af19e6ac922b4ee85fe701408968dfd")) + (let ((commit "84cbf35adbb15c79638372d108308edb05f12683")) (package (inherit genenetwork2) (name "python3-genenetwork2") (version (string-append "3.11-guix-" (string-take commit 7) )) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/genenetwork/genenetwork2.git") + (commit commit))) + (file-name (string-append name "-" version)) + (sha256 + (base32 + "1402g129ghfh0xwfxjj1i7gbib2yl9rahf55caj7b1psy24ys87x")))) (propagated-inputs (let ((inputs (package-propagated-inputs genenetwork2))) `(,@(fold @@ -459,8 +468,10 @@ implemented, light on server resource usage, and fairly speedy.") (filter (lambda (x) (let ((name (car x))) (or (string-prefix? "python2" name) - (string-prefix? "python-2" name)))) + (string-prefix? "python-2" name) + (string=? "python" name)))) inputs))) + ("python" ,python-wrapper) ("python-pillow" ,python-pillow) ("python-coverage" ,python-coverage) ("python-flask" ,python-flask) @@ -478,57 +489,38 @@ implemented, light on server resource usage, and fairly speedy.") ("python-mysqlclient" ,python-mysqlclient) ("python-numpy" ,python-numpy) ("python-pandas" ,python-pandas) - ("python-mock" ,python-mock) ("python-parameterized" ,python-parameterized) ("python-passlib" ,python-passlib) ("python-redis" ,python-redis) ("python-requests" ,python-requests) ("python-simplejson" ,python-simplejson) ("python-pyyaml" ,python-pyyaml) - ("python-unittest2" ,python-unittest2) ("python-xlsxwriter" ,python-xlsxwriter)))) (arguments - `(#:python ,python - #:phases - (modify-phases %standard-phases - (delete 'reset-gzip-timestamps) - (add-after 'unpack 'fix-paths-scripts - (lambda _ - (substitute* "bin/genenetwork2" - (("/usr/bin/env") (which "env")) - (("python ") (string-append (which "python3") " ")) - (("readlink") (which "readlink")) - (("dirname") (which "dirname")) - (("basename") (which "basename")) - (("cat") (which "cat")) - (("echo") (which "echo")) - (("redis-server") (which "redis-server")) - (("git") (which "git")) - (("grep") (which "grep")) - (("rm") (which "rm")) - (("which") (which "which")) ; three whiches in a row! - ) - #t)) - (add-after 'unpack 'patch-javascript - (lambda* (#:key inputs #:allow-other-keys) - (let ((colorbox (assoc-ref inputs "javascript-colorbox")) - (gn2 "/share/genenetwork2/javascript/")) - (delete-file-recursively "wqflask/wqflask/static/packages/colorbox") - (copy-recursively colorbox "wqflask/wqflask/static/packages/colorbox") - #t))) - (add-before 'install 'fix-paths - (lambda* (#:key inputs #:allow-other-keys) - (let* ( - (plink2cmd (string-append (assoc-ref inputs "plink-ng-gn") "/bin/plink2")) - (gemmacmd (string-append (assoc-ref inputs "gemma") "/bin/gemma")) - ) - (substitute* '("etc/default_settings.py") - (("^PLINK_COMMAND =.*") (string-append "PLINK_COMMAND = \"" plink2cmd "\"\n" )) - (("^GEMMA_COMMAND =.*") (string-append "GEMMA_COMMAND = \"" gemmacmd "\"\n" )) - ) - )))) - #:tests? #f)) ; no 'setup.py test' - ))) + (let ((python (specification->package "python-wrapper")) + (args (package-arguments genenetwork2))) + (substitute-keyword-arguments args + ((#:python _) python) + ((#:phases phases) + `(modify-phases ,phases + (add-after 'unpack 'fix-paths-scripts + (lambda _ + (substitute* "bin/genenetwork2" + (("/usr/bin/env") (which "env")) + (("python ") (string-append (which "python3") " ")) + (("readlink") (which "readlink")) + (("dirname") (which "dirname")) + (("basename") (which "basename")) + (("cat") (which "cat")) + (("echo") (which "echo")) + (("redis-server") (which "redis-server")) + (("git") (which "git")) + (("grep") (which "grep")) + (("rm") (which "rm")) + (("which") (which "which"))) + #t)))) + )) + )))) ;; ./pre-inst-env guix download http://files.genenetwork.org/raw_database/db_webqtl_s.zip ;; 0sscjh0wml2lx0mb43vf4chg9gpbfi7abpjxb34n3kyny9ll557x |