From 3ca1d917b6bb0e256c90b7d0d494b0ceebcf196d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 25 Feb 2019 14:56:45 +0100
Subject: 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.
---
 gnu/packages/bioinformatics.scm | 60 ++++++++++++++++++++++++++++-------------
 1 file 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")
-- 
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