diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 122 |
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+))) |