gnu: bamm: Fetch from git and use INVOKE.
* gnu/packages/bioinformatics.scm (bamm)[source]: Fetch from git. [arguments]: Use INVOKE and return #T unconditionally.
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@ -167,15 +167,16 @@ structure of the predicted RNA.")
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(name "bamm")
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(version "1.7.3")
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(source (origin
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(method url-fetch)
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(method git-fetch)
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;; BamM is not available on pypi.
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(uri (string-append
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"https://github.com/Ecogenomics/BamM/archive/"
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version ".tar.gz"))
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(file-name (string-append name "-" version ".tar.gz"))
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(uri (git-reference
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(url "https://github.com/Ecogenomics/BamM.git")
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(commit version)
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(recursive? #t)))
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(file-name (git-file-name name version))
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(sha256
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(base32
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"1f35yxp4pc8aadsvbpg6r4kg2jh4fkjci0iby4iyljm6980sac0s"))
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"1p83ahi984ipslxlg4yqy1gdnya9rkn1v71z8djgxkm9d2chw4c5"))
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(modules '((guix build utils)))
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(snippet
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`(begin
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@ -197,11 +198,12 @@ structure of the predicted RNA.")
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(lambda _
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(with-directory-excursion "c"
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(let ((sh (which "sh")))
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(for-each make-file-writable (find-files "." ".*"))
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;; Use autogen so that 'configure' works.
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(substitute* "autogen.sh" (("/bin/sh") sh))
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(setenv "CONFIG_SHELL" sh)
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(substitute* "configure" (("/bin/sh") sh))
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(zero? (system* "./autogen.sh"))))))
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(invoke "./autogen.sh")))
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#t))
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(delete 'build)
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;; Run tests after installation so compilation only happens once.
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(delete 'check)
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@ -229,7 +231,8 @@ structure of the predicted RNA.")
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;; There are 2 errors printed, but they are safe to ignore:
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;; 1) [E::hts_open_format] fail to open file ...
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;; 2) samtools view: failed to open ...
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(zero? (system* "nosetests")))))))
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(invoke "nosetests")
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#t)))))
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(native-inputs
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`(("autoconf" ,autoconf)
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("automake" ,automake)
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