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gnu: tadbit: Update to 1.0.1-1.5c4c1dd.

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* gnu/packages/bioinformatics.scm (tadbit): Update to 1.0.1-1.5c4c1dd.
[arguments]: Remove trailing #T from build phases; pass -fcommon to test
binaries; run tests conditionally.
This commit is contained in:
Ricardo Wurmus 2021-12-08 16:31:18 +01:00
parent 7f4d25f86e
commit 00ae87c41a
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GPG key ID: 197A5888235FACAC
1 changed files with 59 additions and 53 deletions
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112
gnu/packages/bioinformatics.scm
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@ -9430,66 +9430,72 @@ (define-public imp
(license (list license:lgpl2.1+
license:gpl3+))))
;; We use this seemingly arbitrary commit because of
;; https://github.com/3DGenomes/TADbit/issues/371
(define-public tadbit
(package
(name "tadbit")
(version "1.0.1")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/3DGenomes/TADbit")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"0hqrlymh2a2bimcfdvlssy1x5h1lp3h1c5a7jj11hmcqczzqn3ni"))))
(build-system python-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'fix-problems-with-setup.py
(lambda* (#:key outputs #:allow-other-keys)
;; Don't attempt to install the bash completions to
;; the home directory.
(rename-file "extras/.bash_completion"
"extras/tadbit")
(substitute* "setup.py"
(("\\(path.expanduser\\('~'\\)")
(string-append "(\""
(assoc-ref outputs "out")
"/etc/bash_completion.d\""))
(("extras/\\.bash_completion")
"extras/tadbit"))
#t))
(replace 'check
(lambda* (#:key inputs outputs #:allow-other-keys)
(add-installed-pythonpath inputs outputs)
(invoke "python3" "test/test_all.py")
#t)))))
(native-inputs
`(("glib" ,glib "bin") ;for gtester
("pkg-config" ,pkg-config)))
(inputs
;; TODO: add Chimera for visualization
`(("imp" ,imp)
("mcl" ,mcl)
("python-future" ,python-future)
("python-h5py" ,python-h5py)
("python-scipy" ,python-scipy)
("python-numpy" ,python-numpy)
("python-matplotlib" ,python-matplotlib)
("python-pysam" ,python-pysam)))
(home-page "https://3dgenomes.github.io/TADbit/")
(synopsis "Analyze, model, and explore 3C-based data")
(description
"TADbit is a complete Python library to deal with all steps to analyze,
(let ((commit "5c4c1ddaadfbaf7e6edc58173e46d801093bdc9b")
(revision "1"))
(package
(name "tadbit")
(version (git-version "1.0.1" revision commit))
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/3DGenomes/TADbit")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
"17nwlvjgqpa7x6jgh56m3di61ynaz34kl1jamyv7r2a5rhfcbkla"))))
(build-system python-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'fix-problems-with-setup.py
(lambda* (#:key outputs #:allow-other-keys)
(substitute* "src/test/Makefile"
(("^CFLAGS=") "CFLAGS= -fcommon"))
;; Don't attempt to install the bash completions to
;; the home directory.
(rename-file "extras/.bash_completion"
"extras/tadbit")
(substitute* "setup.py"
(("\\(path.expanduser\\('~'\\)")
(string-append "(\""
(assoc-ref outputs "out")
"/etc/bash_completion.d\""))
(("extras/\\.bash_completion")
"extras/tadbit"))))
(replace 'check
(lambda* (#:key tests? inputs outputs #:allow-other-keys)
(when tests?
(add-installed-pythonpath inputs outputs)
(invoke "python3" "test/test_all.py")))))))
(native-inputs
`(("glib" ,glib "bin") ;for gtester
("pkg-config" ,pkg-config)))
(inputs
;; TODO: add Chimera for visualization
`(("imp" ,imp)
("mcl" ,mcl)
("python-future" ,python-future)
("python-h5py" ,python-h5py)
("python-scipy" ,python-scipy)
("python-numpy" ,python-numpy)
("python-matplotlib" ,python-matplotlib)
("python-pysam" ,python-pysam)))
(home-page "https://3dgenomes.github.io/TADbit/")
(synopsis "Analyze, model, and explore 3C-based data")
(description
"TADbit is a complete Python library to deal with all steps to analyze,
model, and explore 3C-based data. With TADbit the user can map FASTQ files to
obtain raw interaction binned matrices (Hi-C like matrices), normalize and
correct interaction matrices, identify and compare the so-called
@dfn{Topologically Associating Domains} (TADs), build 3D models from the
interaction matrices, and finally, extract structural properties from the
models. TADbit is complemented by TADkit for visualizing 3D models.")
(license license:gpl3+)))
(license license:gpl3+))))
(define-public kentutils
(package