From 026609453176f67d2f28871af114d3d6a9544c2a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 4 Jun 2020 11:54:38 +0200 Subject: [PATCH] gnu: python-pypairix: Update to 0.3.7 and build programs. * gnu/packages/bioinformatics.scm (python-pypairix): Update to 0.3.7. [source]: Fetch from github. [arguments]: Add phases "build-programs" and "install-programs". --- gnu/packages/bioinformatics.scm | 27 ++++++++++++++++++++------- 1 file changed, 20 insertions(+), 7 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 8d1adafd7e..54cdb353c1 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -13788,18 +13788,31 @@ (define-public python-intervaltree (define-public python-pypairix (package (name "python-pypairix") - (version "0.3.6") + (version "0.3.7") + ;; The tarball on pypi does not include the makefile to build the + ;; programs. (source (origin - (method url-fetch) - (uri (pypi-uri "pypairix" version)) + (method git-fetch) + (uri (git-reference + (url "https://github.com/4dn-dcic/pairix.git") + (commit version))) + (file-name (git-file-name name version)) (sha256 (base32 - "0zs92b74s5v4xy2h16s15f3z6l4nnbw8x8zyif7xx5xpafjn0xss")))) + "1snr3lrmsld8sy77ng6ba6wcmd33xjccf1l2f3m6pi29xis9nd6p")))) (build-system python-build-system) - ;; FIXME: the tests fail because test.support cannot be loaded: - ;; ImportError: cannot import name 'support' - (arguments '(#:tests? #f)) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-before 'build 'build-programs + (lambda _ (invoke "make"))) + (add-after 'install 'install-programs + (lambda* (#:key outputs #:allow-other-keys) + (copy-recursively "bin" (string-append + (assoc-ref outputs "out") + "/bin")) + #t))))) (inputs `(("zlib" ,zlib))) (home-page "https://github.com/4dn-dcic/pairix")