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gnu: bamm: Update following changes to the Python build system.

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* gnu/packages/bioinformatics.scm (bamm): Delete trailing #t.
[phases]{check}: Override rather than delete phase.  Remove trailing #t.
{post-install-check}: Delete phase.
{wrap-executable}: Also wrap with the new GUIX_PYTHONPATH.
This commit is contained in:
Maxim Cournoyer 2021-01-22 11:59:08 -05:00
parent 98769a7709
commit 5e47bebf3b
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1 changed files with 15 additions and 31 deletions
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gnu/packages/bioinformatics.scm
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@ -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 @@ (define-public bamm
(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 @@ (define-public bamm
;; 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)