diff options
Diffstat (limited to 'gn/packages')
| -rw-r--r-- | gn/packages/genenetwork.scm | 102 | ||||
| -rw-r--r-- | gn/packages/gn-auth.scm | 69 |
2 files changed, 74 insertions, 97 deletions
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 36d3ae6..6e5bbce 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -463,47 +463,93 @@ (description "Genenetwork installation sumo.") (license license:agpl3+)))) +(define-public gn-auth + (package + (name "gn-auth") + (version "1.0.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/genenetwork/gn-auth.git") + (commit "6b4e800ad2b642d3dce80cdcf84a102aad64fcfd"))) + (hash + (content-hash + (base32 + "036k561kvzb6nwr1k1pd9fi20v4d7cnj5jdps6a30yjprfvj8y4l"))))) + (build-system python-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "pytest" "-k" "unit_test"))))))) + (native-inputs + (list python-mypy + python-pytest + python-pylint + python-hypothesis + python-pytest-mock + python-mypy-extensions)) + (propagated-inputs + (list gunicorn + python-flask + python-redis + python-authlib + python-pymonad + yoyo-migrations + python-bcrypt ;; remove after removing all references + python-mysqlclient + python-argon2-cffi + python-email-validator)) + (home-page "https://github.com/genenetwork/gn-auth") + (synopsis "Authentication and Authorisation server for GeneNetwork services") + (description "Authentication and Authorisation server for GeneNetwork services.") + (license license:agpl3+))) + ;; ./pre-inst-env guix download http://files.genenetwork.org/raw_database/db_webqtl_s.zip ;; 0sscjh0wml2lx0mb43vf4chg9gpbfi7abpjxb34n3kyny9ll557x (define-public genenetwork2-files-small (let ((pfff "xx")) (package - (name "genenetwork2-files-small") - (version "1.0") - (source - (origin - (method url-fetch) - (uri "http://files.genenetwork.org/data_files/gn2_data_s-20160303-C9E672ECED1F51B915DE419B5B2C524E.tar.lz4") - (file-name (string-append name "-" pfff)) - (sha256 - (base32 "058ymx3af6abdhdxyxj0i9qfvb6v7j091frjpp6jh4ahks7r23lj")))) - (build-system trivial-build-system) - (native-inputs `(("lz4" ,lz4) - ("tar" ,tar) - ("source" ,source))) + (name "genenetwork2-files-small") + (version "1.0") + (source + (origin + (method url-fetch) + (uri "http://files.genenetwork.org/data_files/gn2_data_s-20160303-C9E672ECED1F51B915DE419B5B2C524E.tar.lz4") + (file-name (string-append name "-" pfff)) + (sha256 + (base32 "058ymx3af6abdhdxyxj0i9qfvb6v7j091frjpp6jh4ahks7r23lj")))) + (build-system trivial-build-system) + (native-inputs `(("lz4" ,lz4) + ("tar" ,tar) + ("source" ,source))) - (arguments - `(#:modules ((guix build utils)) - #:builder - (let* ((out (assoc-ref %outputs "out")) - (name "gn2_data_s") - (tarfn (string-append name ".tar")) - (targetdir (string-append out "/share/genenetwork2/"))) + (arguments + `(#:modules ((guix build utils)) + #:builder + (let* ((out (assoc-ref %outputs "out")) + (name "gn2_data_s") + (tarfn (string-append name ".tar")) + (targetdir (string-append out "/share/genenetwork2/"))) (begin (use-modules (guix build utils)) (let ((source (assoc-ref %build-inputs "source")) (lz4unpack (string-append (assoc-ref %build-inputs "lz4") "/bin/lz4")) (tar (string-append (assoc-ref %build-inputs "tar") "/bin/tar"))) (and - (zero? (system* lz4unpack source "-d" tarfn)) - (zero? (system* tar "xf" tarfn)) - (mkdir-p targetdir) - (copy-recursively name targetdir))))))) - (home-page "http://genenetwork.org/") - (synopsis "Small file archive to run on genenetwork") - (description "Genenetwork genotype and mapping files.") - (license license:agpl3+)))) + (zero? (system* lz4unpack source "-d" tarfn)) + (zero? (system* tar "xf" tarfn)) + (mkdir-p targetdir) + (copy-recursively name targetdir))))))) + (home-page "http://genenetwork.org/") + (synopsis "Small file archive to run on genenetwork") + (description "Genenetwork genotype and mapping files.") + (license license:agpl3+)))) (define-public genenetwork2-database-small (let ((md5 "93e745e9c")) diff --git a/gn/packages/gn-auth.scm b/gn/packages/gn-auth.scm deleted file mode 100644 index a87b22c..0000000 --- a/gn/packages/gn-auth.scm +++ /dev/null @@ -1,69 +0,0 @@ -(define-module (gn packages gn-auth) - #:use-module (guix) - #:use-module (guix gexp) - #:use-module (guix packages) - #:use-module (guix download) - #:use-module (guix git-download) - #:use-module (guix build-system python) - #:use-module ((guix licenses) #:prefix license:) - - ;; Packages from guix - #:use-module (gnu packages check) - - #:use-module (gnu packages django) - - #:use-module (gnu packages python-web) - #:use-module (gnu packages python-xyz) - #:use-module (gnu packages python-check) - #:use-module (gnu packages python-crypto) - - #:use-module (gnu packages databases) - - ;; Packages from guix-bioinformatics - #:use-module (gn packages python-web)) - -(define-public gn-auth - (package - (name "gn-auth") - (version "1.0.0") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/genenetwork/gn-auth.git") - (commit "6b4e800ad2b642d3dce80cdcf84a102aad64fcfd"))) - (hash - (content-hash - (base32 - "036k561kvzb6nwr1k1pd9fi20v4d7cnj5jdps6a30yjprfvj8y4l"))))) - (build-system python-build-system) - (arguments - (list - #:phases - #~(modify-phases %standard-phases - (replace 'check - (lambda* (#:key tests? #:allow-other-keys) - (when tests? - (invoke "pytest" "-k" "unit_test"))))))) - (native-inputs - (list python-mypy - python-pytest - python-pylint - python-hypothesis - python-pytest-mock - python-mypy-extensions)) - (propagated-inputs - (list gunicorn - python-flask - python-redis - python-authlib - python-pymonad - yoyo-migrations - python-bcrypt ;; remove after removing all references - python-mysqlclient - python-argon2-cffi - python-email-validator)) - (home-page "https://github.com/genenetwork/gn-auth") - (synopsis "Authentication and Authorisation server for GeneNetwork services") - (description "Authentication and Authorisation server for GeneNetwork services.") - (license license:agpl3+))) |