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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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1 changed files with 59 additions and 53 deletions
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@ -9430,25 +9430,32 @@ applications for tackling some common problems in a user-friendly way.")
(license (list license:lgpl2.1+ (license (list license:lgpl2.1+
license:gpl3+)))) license:gpl3+))))
;; We use this seemingly arbitrary commit because of
;; https://github.com/3DGenomes/TADbit/issues/371
(define-public tadbit (define-public tadbit
(let ((commit "5c4c1ddaadfbaf7e6edc58173e46d801093bdc9b")
(revision "1"))
(package (package
(name "tadbit") (name "tadbit")
(version "1.0.1") (version (git-version "1.0.1" revision commit))
(source (origin (source (origin
(method git-fetch) (method git-fetch)
(uri (git-reference (uri (git-reference
(url "https://github.com/3DGenomes/TADbit") (url "https://github.com/3DGenomes/TADbit")
(commit (string-append "v" version)))) (commit commit)))
(file-name (git-file-name name version)) (file-name (git-file-name name version))
(sha256 (sha256
(base32 (base32
"0hqrlymh2a2bimcfdvlssy1x5h1lp3h1c5a7jj11hmcqczzqn3ni")))) "17nwlvjgqpa7x6jgh56m3di61ynaz34kl1jamyv7r2a5rhfcbkla"))))
(build-system python-build-system) (build-system python-build-system)
(arguments (arguments
`(#:phases `(#: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)
(substitute* "src/test/Makefile"
(("^CFLAGS=") "CFLAGS= -fcommon"))
;; 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"
@ -9459,13 +9466,12 @@ applications for tackling some common problems in a user-friendly way.")
(assoc-ref outputs "out") (assoc-ref outputs "out")
"/etc/bash_completion.d\"")) "/etc/bash_completion.d\""))
(("extras/\\.bash_completion") (("extras/\\.bash_completion")
"extras/tadbit")) "extras/tadbit"))))
#t))
(replace 'check (replace 'check
(lambda* (#:key inputs outputs #:allow-other-keys) (lambda* (#:key tests? inputs outputs #:allow-other-keys)
(when tests?
(add-installed-pythonpath inputs outputs) (add-installed-pythonpath inputs outputs)
(invoke "python3" "test/test_all.py") (invoke "python3" "test/test_all.py")))))))
#t)))))
(native-inputs (native-inputs
`(("glib" ,glib "bin") ;for gtester `(("glib" ,glib "bin") ;for gtester
("pkg-config" ,pkg-config))) ("pkg-config" ,pkg-config)))
@ -9489,7 +9495,7 @@ correct interaction matrices, identify and compare the so-called
@dfn{Topologically Associating Domains} (TADs), build 3D models from the @dfn{Topologically Associating Domains} (TADs), build 3D models from the
interaction matrices, and finally, extract structural properties from the interaction matrices, and finally, extract structural properties from the
models. TADbit is complemented by TADkit for visualizing 3D models.") models. TADbit is complemented by TADkit for visualizing 3D models.")
(license license:gpl3+))) (license license:gpl3+))))
(define-public kentutils (define-public kentutils
(package (package