@@ 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")