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gnu: discrover: Replace "texlive" with a texlive-union. 

* gnu/packages/bioinformatics.scm (discrover)[arguments]: Add build phase
"fix-latex-errors"; add build phase "setenv-HOME".
[inputs]: Add rmath-standalone.
[native-inputs]: Replace "texlive" with a texlive-union consisting of
texlive-fonts-cm, texlive-fonts-amsfonts, texlive-generic-ifxetex,
texlive-latex-doi, texlive-latex-examplep, texlive-latex-hyperref,
texlive-latex-ms, texlive-latex-natbib, texlive-bibtex,
texlive-latex-oberdiek, texlive-latex-pgf, texlive-latex-url,
texlive-latex-verbatimbox, and texlive-latex-xcolor.
master
Ricardo Wurmus 2019-02-25 14:56:45 +01:00
parent 5c06a18503
commit 3ca1d917b6
No known key found for this signature in database
GPG Key ID: 197A5888235FACAC
1 changed files with 41 additions and 19 deletions
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gnu/packages/bioinformatics.scm
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@ -2308,6 +2308,23 @@ data and settings.")
`(#:tests? #f ; there are no tests
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'fix-latex-errors
(lambda _
(with-fluids ((%default-port-encoding #f))
(substitute* "doc/references.bib"
(("\\{S\\}illanp[^,]+,")
"{S}illanp{\\\"a}{\\\"a},")))
;; XXX: I just can't get pdflatex to not complain about these
;; characters. They end up in the manual via the generated
;; discrover-cli-help.txt.
(substitute* "src/hmm/cli.cpp"
(("µ") "mu")
(("η") "eta")
(("≤") "<="))
;; This seems to be a syntax error.
(substitute* "doc/discrover-manual.tex"
(("theverbbox\\[t\\]") "theverbbox"))
#t))
(add-after 'unpack 'add-missing-includes
(lambda _
(substitute* "src/executioninformation.hpp"
@ -2316,28 +2333,33 @@ data and settings.")
(substitute* "src/plasma/fasta.hpp"
(("#define FASTA_HPP" line)
(string-append line "\n#include <random>")))
#t)))))
#t))
;; FIXME: this is needed because we're using texlive-union, which
;; doesn't handle fonts correctly. It expects to be able to generate
;; fonts in the home directory.
(add-before 'build 'setenv-HOME
(lambda _ (setenv "HOME" "/tmp") #t)))))
(inputs
`(("boost" ,boost)
("cairo" ,cairo)))
("cairo" ,cairo)
("rmath-standalone" ,rmath-standalone)))
(native-inputs
`(("texlive" ,texlive)
;; TODO: Replace texlive with minimal texlive-union.
;; ("texlive" ,(texlive-union (list texlive-latex-doi
;; texlive-latex-hyperref
;; texlive-latex-oberdiek
;; texlive-generic-ifxetex
;; texlive-latex-url
;; texlive-latex-pgf
;; texlive-latex-examplep
;; texlive-latex-natbib
;; texlive-latex-verbatimbox
;; texlive-latex-ms
;; texlive-latex-xcolor
;; texlive-fonts-amsfonts
;; texlive-latex-amsfonts
;; ;; ...
;; )))
`(("texlive" ,(texlive-union (list texlive-fonts-cm
texlive-fonts-amsfonts
texlive-generic-ifxetex
texlive-latex-doi
texlive-latex-examplep
texlive-latex-hyperref
texlive-latex-ms
texlive-latex-natbib
texlive-bibtex ; style files used by natbib
texlive-latex-oberdiek ; ltxcmds
texlive-latex-pgf ; tikz
texlive-latex-url
texlive-latex-verbatimbox
texlive-latex-xcolor)))
("imagemagick" ,imagemagick)))
(home-page "http://dorina.mdc-berlin.de/public/rajewsky/discrover/")
(synopsis "Discover discriminative nucleotide sequence motifs")