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authorRicardo Wurmus <rekado@elephly.net>2019-02-25 14:56:45 +0100
committerRicardo Wurmus <rekado@elephly.net>2019-02-25 15:05:35 +0100
commit3ca1d917b6bb0e256c90b7d0d494b0ceebcf196d (patch)
tree86823ca0d210a42d25ab773d9548c840ee38d5dc /gnu/packages/bioinformatics.scm
parent5c06a185038ec7e114b71bafdbcab42cca9abcfb (diff)
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.
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
-rw-r--r--gnu/packages/bioinformatics.scm60
1 files changed, 41 insertions, 19 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 5dc3945035..6cea6aeded 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -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")