diff options
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 67 |
1 files changed, 67 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 030327dcf2..152ee22225 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -50,6 +50,8 @@ #:use-module (gnu packages file) #:use-module (gnu packages gawk) #:use-module (gnu packages gcc) + #:use-module (gnu packages gd) + #:use-module (gnu packages image) #:use-module (gnu packages java) #:use-module (gnu packages linux) #:use-module (gnu packages logging) @@ -58,6 +60,7 @@ #:use-module (gnu packages mpi) #:use-module (gnu packages ncurses) #:use-module (gnu packages pcre) + #:use-module (gnu packages pdf) #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) #:use-module (gnu packages popt) @@ -73,6 +76,7 @@ #:use-module (gnu packages vim) #:use-module (gnu packages web) #:use-module (gnu packages xml) + #:use-module (gnu packages xorg) #:use-module (gnu packages zip) #:use-module (srfi srfi-1)) @@ -5472,6 +5476,69 @@ two-dimensional genome scans.") libraries for systems that do not have these available via other means.") (license license:artistic2.0))) +(define-public emboss + (package + (name "emboss") + (version "6.5.7") + (source (origin + (method url-fetch) + (uri (string-append "ftp://emboss.open-bio.org/pub/EMBOSS/old/" + (version-major+minor version) ".0/" + "EMBOSS-" version ".tar.gz")) + (sha256 + (base32 + "0vsmz96gc411yj2iyzdrsmg4l2n1nhgmp7vrgzlxx3xixv9xbf0q")))) + (build-system gnu-build-system) + (arguments + `(#:configure-flags + (list (string-append "--with-hpdf=" + (assoc-ref %build-inputs "libharu"))) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'fix-checks + (lambda _ + ;; The PNGDRIVER tests check for the presence of libgd, libpng + ;; and zlib, but assume that they are all found at the same + ;; prefix. + (substitute* "configure.in" + (("CHECK_PNGDRIVER") + "LIBS=\"$LIBS -lgd -lpng -lz -lm\" +AC_DEFINE([PLD_png], [1], [Define to 1 if PNG support is available]) +AM_CONDITIONAL(AMPNG, true)")) + #t)) + (add-after 'unpack 'disable-update-check + (lambda _ + ;; At build time there is no connection to the Internet, so + ;; looking for updates will not work. + (substitute* "Makefile.am" + (("\\$\\(bindir\\)/embossupdate") "")) + #t)) + (add-before 'configure 'autogen + (lambda _ (zero? (system* "autoreconf" "-vif"))))))) + (inputs + `(("perl" ,perl) + ("libpng" ,libpng) + ("gd" ,gd) + ("libx11" ,libx11) + ("libharu" ,libharu) + ("zlib" ,zlib))) + (native-inputs + `(("autoconf" ,autoconf) + ("automake" ,automake) + ("libtool" ,libtool) + ("pkg-config" ,pkg-config))) + (home-page "http://emboss.sourceforge.net") + (synopsis "Molecular biology analysis suite") + (description "EMBOSS is the \"European Molecular Biology Open Software +Suite\". EMBOSS is an analysis package specially developed for the needs of +the molecular biology (e.g. EMBnet) user community. The software +automatically copes with data in a variety of formats and even allows +transparent retrieval of sequence data from the web. It also provides a +number of libraries for the development of software in the field of molecular +biology. EMBOSS also integrates a range of currently available packages and +tools for sequence analysis into a seamless whole.") + (license license:gpl2+))) + (define-public piranha ;; There is no release tarball for the latest version. The latest commit is ;; older than one year at the time of this writing. |