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gnu: Add NCBI VDB. 

* gnu/packages/bioinformatics.scm (ncbi-vdb): New variable.
This commit is contained in:
Ricardo Wurmus 2015-04-14 14:42:49 +02:00
parent 2651a5e695
commit 75dd242480
1 changed files with 96 additions and 0 deletions
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96
gnu/packages/bioinformatics.scm
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@ -29,6 +29,7 @@
#:use-module (gnu packages)
#:use-module (gnu packages base)
#:use-module (gnu packages compression)
#:use-module (gnu packages file)
#:use-module (gnu packages java)
#:use-module (gnu packages maths)
#:use-module (gnu packages ncurses)
@ -1123,6 +1124,101 @@ simultaneously.")
("ngs-sdk" ,ngs-sdk)))
(synopsis "Java bindings for NGS SDK")))
(define-public ncbi-vdb
(package
(name "ncbi-vdb")
(version "2.4.5-5")
(source
(origin
(method url-fetch)
(uri
(string-append "https://github.com/ncbi/ncbi-vdb/archive/"
version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"1cj8nk6if8sqagv20vx36v566fdvhcaadf0x1ycnbgql6chbs6vy"))))
(build-system gnu-build-system)
(arguments
`(#:parallel-build? #f ; not supported
#:tests? #f ; no "check" target
#:phases
(alist-replace
'configure
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
;; Only replace the version suffix, not the version number in the
;; directory name; fixed in commit 4dbba5c6a809 (no release yet).
(substitute* "setup/konfigure.perl"
(((string-append "\\$\\(subst "
"(\\$\\(VERSION[^\\)]*\\)),"
"(\\$\\([^\\)]+\\)),"
"(\\$\\([^\\)]+\\)|\\$\\@)"
"\\)")
_ pattern replacement target)
(string-append "$(patsubst "
"%" pattern ","
"%" replacement ","
target ")")))
;; Override include path for libmagic
(substitute* "setup/package.prl"
(("name => 'magic', Include => '/usr/include'")
(string-append "name=> 'magic', Include => '"
(assoc-ref inputs "libmagic")
"/include" "'")))
;; Install kdf5 library (needed by sra-tools)
(substitute* "build/Makefile.install"
(("LIBRARIES_TO_INSTALL =")
"LIBRARIES_TO_INSTALL = kdf5.$(VERSION_LIBX) kdf5.$(VERSION_SHLX)"))
;; The 'configure' script doesn't recognize things like
;; '--enable-fast-install'.
(zero? (system*
"./configure"
(string-append "--build-prefix=" (getcwd) "/build")
(string-append "--prefix=" (assoc-ref outputs "out"))
(string-append "--debug")
(string-append "--with-xml2-prefix="
(assoc-ref inputs "libxml2"))
(string-append "--with-ngs-sdk-prefix="
(assoc-ref inputs "ngs-sdk"))
(string-append "--with-ngs-java-prefix="
(assoc-ref inputs "ngs-java"))
(string-append "--with-hdf5-prefix="
(assoc-ref inputs "hdf5"))))))
(alist-cons-after
'install 'install-interfaces
(lambda* (#:key system outputs #:allow-other-keys)
;; Install interface libraries
(mkdir (string-append (assoc-ref outputs "out") "/ilib"))
(copy-recursively (string-append "build/ncbi-vdb/linux/gcc/"
(car (string-split system #\-))
"/rel/ilib")
(string-append (assoc-ref outputs "out")
"/ilib"))
;; Install interface headers
(copy-recursively "interfaces"
(string-append (assoc-ref outputs "out")
"/include")))
%standard-phases))))
(inputs
`(("libxml2" ,libxml2)
("ngs-sdk" ,ngs-sdk)
("ngs-java" ,ngs-java)
("libmagic" ,file)
("hdf5" ,hdf5)))
(native-inputs `(("perl" ,perl)))
(home-page "https://github.com/ncbi/ncbi-vdb")
(synopsis "Database engine for genetic information")
(description
"The NCBI-VDB library implements a highly compressed columnar data
warehousing engine that is most often used to store genetic information.
Databases are stored in a portable image within the file system, and can be
accessed/downloaded on demand across HTTP.")
(license license:public-domain)))
(define-public seqan
(package
(name "seqan")