;;; GNU Guix --- Functional package management for GNU
  Copyright © 2015 - 2022   <  >
;;;
;;; This file is NOT part of GNU Guix, but is supposed to be used with GNU
;;; Guix and thus has the same license.
;;;
  GNU  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.
;;;
;;; GNU Guix 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 GNU  .   If not , see < / > .

(define-module (bimsb packages legacy)
  #:use-module ((guix licenses) #:prefix license:)
  #:use-module (guix packages)
  #:use-module (guix download)
  #:use-module (guix git-download)
  #:use-module (guix utils)
  #:use-module (guix build utils)
  #:use-module (guix build-system python)
  #:use-module (gnu packages bioinformatics)
  #:use-module (gnu packages maths)
  #:use-module (gnu packages python)
  #:use-module (gnu packages python-build)
  #:use-module (gnu packages python-science)
  #:use-module (gnu packages python-xyz))

(define-public python-mirnylib
  (let ((commit "2d27793111b63ac7d5f82ba3369f927c6c9745da")
        (revision "2"))
    (package
      (name "python-mirnylib")
      (version (git-version "0" revision commit))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "-legacy")
                      (commit commit)))
                (sha256
                 (base32
                  "15s3755f17lnayx1vrpr9pd5wra9kc083f1d8s2qivww5gdxim6q"))))
      (build-system python-build-system)
      (arguments '(#:tests? #f)) ; tests expect additional test data
      (inputs (list hdf5)) ; FIXME: probably should be propagated by h5py
      (propagated-inputs
       (list python-biopython
             python-joblib
             python-bx-python
             python-numpy
             python-scipy
             python-pysam
             python-matplotlib
             python-h5py))
      (native-inputs
       (list python-cython python-setuptools))
      (home-page "-legacy")
      (synopsis "Libraries shared between different mirnylab projects")
      (description
       "This package provides assorted libraries used by different mirnylab
projects.")
      (license license:expat))))

(define-public python2-mirnylib
  (deprecated-package "python2-mirnylib" python-mirnylib))

(define-public python-hiclib
  (let ((commit "518546e41987dca8a40f45ddc63601a5aaf46bfa")
        (revision "4"))
    (package
      (name "python-hiclib")
      (version (git-version "0" revision commit))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "-legacy")
                      (commit commit)))
                (sha256
                 (base32
                  "04zd0hwgb3sw7y9ylp409nnkskpnyij55db2lkvlw7fszc5zdf9k"))))
      (build-system python-build-system)
      (arguments
       `(#:tests? #f ; tests depend on unavailable test data
         #:phases
         (modify-phases %standard-phases
           (add-after 'unpack 'set-matplotlib-backend-to-agg
            (lambda _
  Set the matplotlib backend to Agg to avoid problems using the
  GTK backend without a display .
              (substitute* (find-files "tests" "\\.py")
                (("import matplotlib\\.pyplot as plt" line)
                 (string-append "import matplotlib;matplotlib.use('Agg');"
                                line)))
              #t)))))
      (propagated-inputs
       `(("hdf5" ,hdf5) ; FIXME: probably should be propagated by h5py
         ("python-biopython" ,python-biopython)
         ("python-numpy" ,python-numpy)
         ("python-scipy" ,python-scipy)
         ("python-matplotlib" ,python-matplotlib)
         ("python-pysam" ,python-pysam)
         ("python-mirnylib" ,python-mirnylib)))
      (native-inputs
       `(("python-cython" ,python-cython)
         ("python-setuptools" ,python-setuptools)))
      (home-page "")
      (synopsis "Collection of tools to map, filter and analyze Hi-C data")
      (description
       "Hi-C lib is a collection of tools to map, filter and analyze Hi-C
data.")
      (license license:expat))))

(define-public python2-hiclib
  (deprecated-package "python2-hiclib" python-hiclib))

 GNU Guix --- Functional package management for GNU

 This file is NOT part of GNU Guix, but is supposed to be used with GNU
 Guix and thus has the same license.

 you can redistribute it and/or modify it
 either version 3 of the License , or ( at
 your option) any later version.

 GNU Guix 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.

 tests expect additional test data
 FIXME: probably should be propagated by h5py
 tests depend on unavailable test data
 FIXME: probably should be propagated by h5py
  Copyright © 2015 - 2022   <  >
  under the terms of the GNU General Public License as published by
  You should have received a copy of the GNU General Public License
  along with GNU  .   If not , see < / > .

(define-module (bimsb packages legacy)
  #:use-module ((guix licenses) #:prefix license:)
  #:use-module (guix packages)
  #:use-module (guix download)
  #:use-module (guix git-download)
  #:use-module (guix utils)
  #:use-module (guix build utils)
  #:use-module (guix build-system python)
  #:use-module (gnu packages bioinformatics)
  #:use-module (gnu packages maths)
  #:use-module (gnu packages python)
  #:use-module (gnu packages python-build)
  #:use-module (gnu packages python-science)
  #:use-module (gnu packages python-xyz))

(define-public python-mirnylib
  (let ((commit "2d27793111b63ac7d5f82ba3369f927c6c9745da")
        (revision "2"))
    (package
      (name "python-mirnylib")
      (version (git-version "0" revision commit))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "-legacy")
                      (commit commit)))
                (sha256
                 (base32
                  "15s3755f17lnayx1vrpr9pd5wra9kc083f1d8s2qivww5gdxim6q"))))
      (build-system python-build-system)
      (propagated-inputs
       (list python-biopython
             python-joblib
             python-bx-python
             python-numpy
             python-scipy
             python-pysam
             python-matplotlib
             python-h5py))
      (native-inputs
       (list python-cython python-setuptools))
      (home-page "-legacy")
      (synopsis "Libraries shared between different mirnylab projects")
      (description
       "This package provides assorted libraries used by different mirnylab
projects.")
      (license license:expat))))

(define-public python2-mirnylib
  (deprecated-package "python2-mirnylib" python-mirnylib))

(define-public python-hiclib
  (let ((commit "518546e41987dca8a40f45ddc63601a5aaf46bfa")
        (revision "4"))
    (package
      (name "python-hiclib")
      (version (git-version "0" revision commit))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "-legacy")
                      (commit commit)))
                (sha256
                 (base32
                  "04zd0hwgb3sw7y9ylp409nnkskpnyij55db2lkvlw7fszc5zdf9k"))))
      (build-system python-build-system)
      (arguments
         #:phases
         (modify-phases %standard-phases
           (add-after 'unpack 'set-matplotlib-backend-to-agg
            (lambda _
  Set the matplotlib backend to Agg to avoid problems using the
  GTK backend without a display .
              (substitute* (find-files "tests" "\\.py")
                (("import matplotlib\\.pyplot as plt" line)
                 (string-append "import matplotlib;matplotlib.use('Agg');"
                                line)))
              #t)))))
      (propagated-inputs
         ("python-biopython" ,python-biopython)
         ("python-numpy" ,python-numpy)
         ("python-scipy" ,python-scipy)
         ("python-matplotlib" ,python-matplotlib)
         ("python-pysam" ,python-pysam)
         ("python-mirnylib" ,python-mirnylib)))
      (native-inputs
       `(("python-cython" ,python-cython)
         ("python-setuptools" ,python-setuptools)))
      (home-page "")
      (synopsis "Collection of tools to map, filter and analyze Hi-C data")
      (description
       "Hi-C lib is a collection of tools to map, filter and analyze Hi-C
data.")
      (license license:expat))))

(define-public python2-hiclib
  (deprecated-package "python2-hiclib" python-hiclib))
