* gnu/packages/bioinformatics.scm (ncbi-tools): New variable.
---
gnu/packages/bioinformatics.scm | 62 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 62 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 415024f..961f0b2 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -80,6 +80,7 @@
#:use-module (gnu packages readline)
#:use-module (gnu packages ruby)
#:use-module (gnu packages serialization)
+ #:use-module (gnu packages shells)
#:use-module (gnu packages statistics)
#:use-module (gnu packages tbb)
#:use-module (gnu packages tex)
@@ -4340,6 +4341,67 @@ simultaneously.")
("ngs-sdk" ,ngs-sdk)))
(synopsis "Java bindings for NGS SDK")))
+(define-public ncbi-tools
+ (package
+ (name "ncbi-tools")
+ (version "20160908")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/old/";
+ version "/ncbi.tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1252s4fw41w5yalz9b50pvzvkiyjfcgy0isw1qgmg0v66bp49khz"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ; There are no tests.
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure)
+ (add-after 'unpack 'patch-sources
+ (lambda _
+ (for-each (lambda (file)
+ (substitute* file
+ (("NCBI_MAKE_SHELL = .*")
+ (string-append
+ "NCBI_MAKE_SHELL = "
+ (which "sh")
+ "\n"))))
+ (find-files "platform" ".*mk"))
+ (substitute* "make/ln-if-absent"
+ (("set path=\\(/usr/bin /bin\\)") ""))
+ #t))
+ (replace 'build
+ (lambda _
+ (chdir "..")
+ (zero? (system* "ncbi/make/makedis.csh"))))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (bin (string-append out "/bin"))
+ (man (string-append out "/share/man/man1")))
+ (for-each (lambda (file)
+ (install-file
+ (string-append "ncbi/build/" file) bin)
+ (install-file
+ (string-append "ncbi/doc/man/" file ".1") man))
+ ;; XXX: TODO: Install and test other binaries.
+ (list "tbl2asn"))
+ #t))))))
+ (native-inputs
+ `(("csh" ,tcsh)
+ ("pkg-config" ,pkg-config)
+ ("coreutils" ,coreutils)))
+ (home-page "https://www.ncbi.nlm.nih.gov/IEB/ToolBox/MainPage/index.html";)
+ (synopsis "NCBI-related tools")
+ (description "The United States of America @dfn{National Center for
+Biotechnology Information} (NCBI) Software Development Toolkit is for the
+production and distribution of GenBank, Entrez, BLAST and related NCBI
+services.")
+ (license license:public-domain)))
+
(define-public ncbi-vdb
(package
(name "ncbi-vdb")
--
2.10.2
