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-rw-r--r--gnu/packages/bioinformatics.scm122
1 files changed, 101 insertions, 21 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 5dc3945035..23976ceda0 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 +2333,28 @@ 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-latex-doi
+ texlive-latex-examplep
+ texlive-latex-hyperref
+ texlive-latex-ms
+ texlive-latex-natbib
+ texlive-bibtex ; style files used by natbib
+ texlive-latex-pgf ; tikz
+ texlive-latex-verbatimbox)))
("imagemagick" ,imagemagick)))
(home-page "http://dorina.mdc-berlin.de/public/rajewsky/discrover/")
(synopsis "Discover discriminative nucleotide sequence motifs")
@@ -2693,6 +2710,11 @@ results. The FASTX-Toolkit tools perform some of these preprocessing tasks.")
(arguments
`(#:phases
(modify-phases %standard-phases
+ (add-after 'unpack 'do-not-tune-to-CPU
+ (lambda _
+ (substitute* "src/CMakeLists.txt"
+ ((" -march=native") ""))
+ #t))
(replace 'check
(lambda* (#:key outputs #:allow-other-keys)
(setenv "PATH" (string-append (getcwd) ":" (getenv "PATH")))
@@ -12880,7 +12902,7 @@ expression report comparing samples in an easily configurable manner.")
(define-public pigx-chipseq
(package
(name "pigx-chipseq")
- (version "0.0.20")
+ (version "0.0.21")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/BIMSBbioinfo/pigx_chipseq/"
@@ -12888,7 +12910,7 @@ expression report comparing samples in an easily configurable manner.")
"/pigx_chipseq-" version ".tar.gz"))
(sha256
(base32
- "19a7dclqq0b4kqg3phiz4d4arlwfp34nm3z0rf1gkqdpsy7gghp3"))))
+ "0psgdzlnx5xwhlhpss5yvmnl7yv19y9742l97m04f7awd8w74gxs"))))
(build-system gnu-build-system)
;; parts of the tests rely on access to the network
(arguments '(#:tests? #f))
@@ -14403,3 +14425,61 @@ datasets. A popular implementation of t-SNE uses the Barnes-Hut algorithm to
approximate the gradient at each iteration of gradient descent. This package
is a Cython wrapper for FIt-SNE.")
(license license:bsd-4)))
+
+(define-public velvet
+ (package
+ (name "velvet")
+ (version "1.2.10")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "https://www.ebi.ac.uk/~zerbino/velvet/"
+ "velvet_" version ".tgz"))
+ (sha256
+ (base32
+ "0h3njwy66p6bx14r3ar1byb0ccaxmxka4c65rn4iybyiqa4d8kc8"))
+ ;; Delete bundled libraries
+ (modules '((guix build utils)))
+ (snippet
+ '(begin
+ (delete-file "Manual.pdf")
+ (delete-file-recursively "third-party")
+ #t))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:make-flags '("OPENMP=t")
+ #:test-target "test"
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure)
+ (add-after 'unpack 'fix-zlib-include
+ (lambda _
+ (substitute* "src/binarySequences.c"
+ (("../third-party/zlib-1.2.3/zlib.h") "zlib.h"))
+ #t))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (bin (string-append out "/bin"))
+ (doc (string-append out "/share/doc/velvet")))
+ (mkdir-p bin)
+ (mkdir-p doc)
+ (install-file "velveth" bin)
+ (install-file "velvetg" bin)
+ (install-file "Manual.pdf" doc)
+ (install-file "Columbus_manual.pdf" doc)
+ #t))))))
+ (inputs
+ `(("openmpi" ,openmpi)
+ ("zlib" ,zlib)))
+ (native-inputs
+ `(("texlive" ,(texlive-union (list texlive-latex-graphics
+ texlive-latex-hyperref)))))
+ (home-page "https://www.ebi.ac.uk/~zerbino/velvet/")
+ (synopsis "Nucleic acid sequence assembler for very short reads")
+ (description
+ "Velvet is a de novo genomic assembler specially designed for short read
+sequencing technologies, such as Solexa or 454. Velvet currently takes in
+short read sequences, removes errors then produces high quality unique
+contigs. It then uses paired read information, if available, to retrieve the
+repeated areas between contigs.")
+ (license license:gpl2+)))