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Re: [PATCH 2/4] gnu: Add ncbi-tools.
From: |
Marius Bakke |
Subject: |
Re: [PATCH 2/4] gnu: Add ncbi-tools. |
Date: |
Sat, 03 Dec 2016 20:30:04 +0100 |
User-agent: |
Notmuch/0.23.3 (https://notmuchmail.org) Emacs/25.1.1 (x86_64-unknown-linux-gnu) |
Ben Woodcroft <address@hidden> writes:
> * 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"))
I'm getting a timeout on this, though it works in a browser. However
this server is apparently also available over HTTPS, which is better.
> + (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)))
The files in regexp/ are released under a custom license found in
regexp/doc/LICENSE. Also corelib/regex.{c.h} are GPL2+.
algo/blast/core/boost_erf.c is covered by boost1.0, and
connect/parson.{c,h} are MIT. Some files in connect/mitsock seems to be
covered by an early variant of the 2-clause BSD.
Other files have unclear license terms such as those in
corelib/morefiles, though they seem sufficiently free for the
non-copyleft procedure. LGTM with these updates!
> +
> (define-public ncbi-vdb
> (package
> (name "ncbi-vdb")
> --
> 2.10.2
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