diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 46 |
1 files changed, 15 insertions, 31 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f7d6a6b38f..85aaeb30e6 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12,7 +12,7 @@ ;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com> ;;; Copyright © 2018 Gábor Boskovits <boskovits@gmail.com> ;;; Copyright © 2018, 2019, 2020 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> -;;; Copyright © 2019, 2020 Maxim Cournoyer <maxim.cournoyer@gmail.com> +;;; Copyright © 2019, 2020, 2021 Maxim Cournoyer <maxim.cournoyer@gmail.com> ;;; Copyright © 2019 Brian Leung <bkleung89@gmail.com> ;;; Copyright © 2019 Brett Gilio <brettg@gnu.org> ;;; Copyright © 2020 Björn Höfling <bjoern.hoefling@bjoernhoefling.de> @@ -208,8 +208,7 @@ structure of the predicted RNA.") (snippet `(begin ;; Delete bundled htslib. - (delete-file-recursively "c/htslib-1.3.1") - #t)))) + (delete-file-recursively "c/htslib-1.3.1"))))) (build-system python-build-system) (arguments `(#:python ,python-2 ; BamM is Python 2 only. @@ -229,37 +228,22 @@ structure of the predicted RNA.") ;; Use autogen so that 'configure' works. (substitute* "autogen.sh" (("/bin/sh") sh)) (setenv "CONFIG_SHELL" sh) - (invoke "./autogen.sh"))) - #t)) - (delete 'build) - ;; Run tests after installation so compilation only happens once. - (delete 'check) - (add-after 'install 'wrap-executable - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (path (getenv "PATH"))) - (wrap-program (string-append out "/bin/bamm") - `("PATH" ":" prefix (,path)))) - #t)) - (add-after 'wrap-executable 'post-install-check - (lambda* (#:key inputs outputs #:allow-other-keys) - (setenv "PATH" - (string-append (assoc-ref outputs "out") - "/bin:" - (getenv "PATH"))) - (setenv "PYTHONPATH" - (string-append - (assoc-ref outputs "out") - "/lib/python" - (string-take (string-take-right - (assoc-ref inputs "python") 5) 3) - "/site-packages:" - (getenv "PYTHONPATH"))) + (invoke "./autogen.sh"))))) + (delete 'build) ;the build loops otherwise + (replace 'check + (lambda _ ;; There are 2 errors printed, but they are safe to ignore: ;; 1) [E::hts_open_format] fail to open file ... ;; 2) samtools view: failed to open ... - (invoke "nosetests") - #t))))) + (invoke "nosetests"))) + (add-after 'install 'wrap-executable + (lambda* (#:key inputs outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (path (getenv "PATH")) + (pythonpath (getenv "GUIX_PYTHONPATH"))) + (wrap-program (string-append out "/bin/bamm") + `("PATH" ":" prefix (,path)) + `("GUIX_PYTHONPATH" ":" prefix (,pythonpath))))))))) (native-inputs `(("autoconf" ,autoconf) ("automake" ,automake) |