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gnu: Add EMBOSS.

* gnu/packages/bioinformatics.scm (emboss): New variable.
gn-latest-20200428
Ricardo Wurmus 5 years ago
parent
commit
66e40e0065
No known key found for this signature in database GPG Key ID: 197A5888235FACAC
  1. 67
      gnu/packages/bioinformatics.scm

67
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.

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