[PATCH 2/4] gnu: Add ncbi-tools.

[Ben Woodcroft]

* 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