diff options
| author | Ricardo Wurmus <rekado@elephly.net> | 2019-02-25 14:56:45 +0100 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2019-02-25 15:05:35 +0100 |
| commit | 3ca1d917b6bb0e256c90b7d0d494b0ceebcf196d (patch) | |
| tree | 86823ca0d210a42d25ab773d9548c840ee38d5dc /gnu/packages/bioinformatics.scm | |
| parent | 5c06a185038ec7e114b71bafdbcab42cca9abcfb (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.scm | 60 |
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") |