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gnu: tadbit: Update to 1.0.1.

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* gnu/packages/bioinformatics.scm (tadbit): Update to 1.0.1.
[arguments]: Remove #:tests? and #:python arguments.
[phases]{fix-problems-with-setup.py}: Remove no longer needed steps.
{check}: Override phase.
[native-inputs]: Add glib and pkg-config.
[inputs]: Add python-future and python-h5py.
This commit is contained in:
Maxim Cournoyer 2020-11-24 02:15:16 -05:00
parent e7e73f750f
commit 4efbf56e53
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GPG key ID: 1260E46482E63562
1 changed files with 18 additions and 15 deletions
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gnu/packages/bioinformatics.scm
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@ -66,6 +66,7 @@
#:use-module (gnu packages boost) #:use-module (gnu packages boost)
#:use-module (gnu packages check) #:use-module (gnu packages check)
#:use-module (gnu packages code) #:use-module (gnu packages code)
#:use-module (gnu packages commencement)
#:use-module (gnu packages cmake) #:use-module (gnu packages cmake)
#:use-module (gnu packages compression) #:use-module (gnu packages compression)
#:use-module (gnu packages cpio) #:use-module (gnu packages cpio)
@ -11227,7 +11228,7 @@ applications for tackling some common problems in a user-friendly way.")
(define-public tadbit (define-public tadbit
(package (package
(name "tadbit") (name "tadbit")
(version "0.2.0") (version "1.0.1")
(source (origin (source (origin
(method git-fetch) (method git-fetch)
(uri (git-reference (uri (git-reference
@ -11236,21 +11237,13 @@ applications for tackling some common problems in a user-friendly way.")
(file-name (git-file-name name version)) (file-name (git-file-name name version))
(sha256 (sha256
(base32 (base32
"07g3aj648prmsvxp9caz5yl41k0y0647vxh0f5p3w8376mfiljd0")))) "0hqrlymh2a2bimcfdvlssy1x5h1lp3h1c5a7jj11hmcqczzqn3ni"))))
(build-system python-build-system) (build-system python-build-system)
(arguments (arguments
`(;; Tests are included and must be run after installation, but `(#:phases
;; they are incomplete and thus cannot be run.
#:tests? #f
#:python ,python-2
#:phases
(modify-phases %standard-phases (modify-phases %standard-phases
(add-after 'unpack 'fix-problems-with-setup.py (add-after 'unpack 'fix-problems-with-setup.py
(lambda* (#:key outputs #:allow-other-keys) (lambda* (#:key outputs #:allow-other-keys)
;; setup.py opens these files for writing
(chmod "_pytadbit/_version.py" #o664)
(chmod "README.rst" #o664)
;; Don't attempt to install the bash completions to ;; Don't attempt to install the bash completions to
;; the home directory. ;; the home directory.
(rename-file "extras/.bash_completion" (rename-file "extras/.bash_completion"
@ -11262,15 +11255,25 @@ applications for tackling some common problems in a user-friendly way.")
"/etc/bash_completion.d\"")) "/etc/bash_completion.d\""))
(("extras/\\.bash_completion") (("extras/\\.bash_completion")
"extras/tadbit")) "extras/tadbit"))
#t))
(replace 'check
(lambda* (#:key inputs outputs #:allow-other-keys)
(add-installed-pythonpath inputs outputs)
(invoke "python3" "test/test_all.py")
#t))))) #t)))))
(native-inputs
`(("glib" ,glib "bin") ;for gtester
("pkg-config" ,pkg-config)))
(inputs (inputs
;; TODO: add Chimera for visualization ;; TODO: add Chimera for visualization
`(("imp" ,imp) `(("imp" ,imp)
("mcl" ,mcl) ("mcl" ,mcl)
("python2-scipy" ,python2-scipy) ("python-future" ,python-future)
("python2-numpy" ,python2-numpy) ("python-h5py" ,python-h5py)
("python2-matplotlib" ,python2-matplotlib) ("python-scipy" ,python-scipy)
("python2-pysam" ,python2-pysam))) ("python-numpy" ,python-numpy)
("python-matplotlib" ,python-matplotlib)
("python-pysam" ,python-pysam)))
(home-page "https://3dgenomes.github.io/TADbit/") (home-page "https://3dgenomes.github.io/TADbit/")
(synopsis "Analyze, model, and explore 3C-based data") (synopsis "Analyze, model, and explore 3C-based data")
(description (description