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;;; guix.scm --- genenetwork3 rest Api guix bootstrapping file.
;;;
;;; Copyright © 2021 Bonface Munyoki Kilyungi <me@bonfacemunyoki.com>
;;;
;;; This file is part of genenetwork3.
;;;
;;; genenetwork3 is free software: you can redistribute it and/or
;;; modify it under the terms of the GNU General Public License as
;;; published by the Free Software Foundation; either version 3 of the
;;; License, or (at your option) any later version.
;;;
;;; sheepdog is distributed in the hope that it will be useful, but
;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
;;; General Public License for more details.
;;;
;;; You should have received a copy of the GNU General Public License
;;; along with genenetwork3. If not, see https://www.gnu.org/licenses/.
(use-modules
(srfi srfi-1)
(srfi srfi-26)
(ice-9 match)
(ice-9 popen)
(ice-9 rdelim)
(gn packages gemma)
(gnu packages base)
(gnu packages check)
(gnu packages databases)
(gnu packages statistics)
(gnu packages python)
(gnu packages python-check)
(gnu packages python-crypto)
(gnu packages python-web)
(gnu packages python-xyz)
(gnu packages python-science)
((guix build utils) #:select (with-directory-excursion))
(guix build-system python)
(guix gexp)
(guix git-download)
(guix licenses)
(guix packages))
(define %source-dir (dirname (current-filename)))
(define git-file?
(let* ((pipe (with-directory-excursion %source-dir
(open-pipe* OPEN_READ "git" "ls-files")))
(files (let loop ((lines '()))
(match (read-line pipe)
((? eof-object?)
(reverse lines))
(line
(loop (cons line lines))))))
(status (close-pipe pipe)))
(lambda (file stat)
(match (stat:type stat)
('directory #t)
((or 'regular 'symlink)
(any (cut string-suffix? <> file) files))
(_ #f)))))
(package
(name "genenetwork3.git")
(version "0.0.1")
(source (local-file %source-dir
#:recursive? #t
#:select? git-file?))
(propagated-inputs `(("coreutils" ,coreutils)
("gemma-wrapper" ,gemma-wrapper)
("python-bcrypt" ,python-bcrypt)
("python" ,python-wrapper)
("python-flask" ,python-flask)
("python-pylint" python-pylint)
("python-numpy" ,python-numpy)
("python-mypy" ,python-mypy)
("python-mypy-extensions" ,python-mypy-extensions)
("python-redis" ,python-redis)
("python-scipy" ,python-scipy)
;; Remove one of these!
("python-sqlalchemy" ,python-sqlalchemy)
("python-mysqlclient" ,python-mysqlclient)
;; This requires R in it's path
;; TODO: Remove!
("python-rpy2" ,python-rpy2)))
(build-system python-build-system)
(home-page "https://github.com/genenetwork/genenetwork3")
(synopsis "GeneNetwork3 API for data science and machine learning.")
(description "GeneNetwork3 API for data science and machine learning.")
(license agpl3+))
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