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gnu: pigx-chipseq: Update to 0.1.0.
* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.1.0. [source]: Remove patch. [arguments]: Remove 'autoreconf phase. [native-inputs]: Remove autoconf and automake. * gnu/packages/patches/pigx-chipseq-no-citeproc.patch: Remove file. * gnu/local.mk (dist_patch_DATA): Remove patch.
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3 changed files with 3 additions and 50 deletions
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@ -10526,7 +10526,7 @@ expression report comparing samples in an easily configurable manner.")
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(define-public pigx-chipseq
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(package
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(name "pigx-chipseq")
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(version "0.0.53")
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(version "0.1.0")
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(source (origin
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(method url-fetch)
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(uri (string-append "https://github.com/BIMSBbioinfo/pigx_chipseq/"
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@ -10534,25 +10534,12 @@ expression report comparing samples in an easily configurable manner.")
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"/pigx_chipseq-" version ".tar.gz"))
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(sha256
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(base32
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"0c6npx35sszycf059w1x1k4k9hq1qqxny0i4p57q1188czr4561h"))
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(patches (search-patches "pigx-chipseq-no-citeproc.patch"))))
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"008n6drj9q5av86xihxlj4py2c9p3c5z5ld89c3bksrp77zxiy67"))))
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(build-system gnu-build-system)
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(arguments
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`(#:tests? #f ; parts of the tests rely on access to the network
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#:phases
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(modify-phases %standard-phases
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(add-before 'bootstrap 'autoreconf
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(lambda _
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;; This was fixed in commit
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;; 0b1c9f7f2e4d0ff601f1de95ab8b2953f4d5dbc7, but there is no
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;; release with this fix.
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(call-with-output-file "VERSION"
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(lambda (port) (display ,version port)))
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;; See https://github.com/BIMSBbioinfo/pigx_chipseq/issues/176
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(substitute* "m4/ax_r_package.m4"
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(("if\\(is.na\\(packageDescription\\(\"PKG\"\\)\\)\\)")
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"if(system.file(package=\"PKG\") == \"\")"))
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(invoke "autoreconf" "-vif")))
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(add-before 'configure 'set-PYTHONPATH
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(lambda _
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(setenv "PYTHONPATH" (getenv "GUIX_PYTHONPATH")))))))
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@ -10606,7 +10593,7 @@ expression report comparing samples in an easily configurable manner.")
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bedtools
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kentutils))
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(native-inputs
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(list autoconf automake python-pytest))
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(list python-pytest))
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(home-page "https://bioinformatics.mdc-berlin.de/pigx/")
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(synopsis "Analysis pipeline for ChIP sequencing experiments")
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(description "PiGX ChIPseq is an analysis pipeline for preprocessing, peak
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