diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 96 |
1 files changed, 96 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 4c4eedba2b..f2f4355d87 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -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") |