Initial import

3 files changed, 198 insertions, 0 deletions

diff --git a/.SRCINFO b/.SRCINFO
new file mode 100644
index 000000000000..b4aa69a69f16
--- /dev/null
+++ b/.SRCINFO
@@ -0,0 +1,34 @@
+pkgbase = ncbi-toolkit
+	pkgdesc = Applications, scripts and C++ libraries for the analysis of biological data
+	pkgver = 9.0.0
+	pkgrel = 1
+	url = http://www.ncbi.nlm.nih.gov/books/NBK7160/
+	arch = i686
+	arch = x86_64
+	license = custom
+	makedepends = autoconf
+	depends = python2
+	depends = pcre
+	depends = sqlite
+	depends = lzo2
+	depends = libtiff
+	depends = giflib
+	depends = libxpm
+	depends = libmysqlclient
+	depends = libpng
+	depends = gnutls
+	depends = libxml2
+	depends = libxslt
+	optdepends = fltk
+	optdepends = wxgtk
+	optdepends = db48
+	optdepends = fcgi
+	provides = blast+-bin
+	conflicts = blast+-bin
+	source = ftp://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools++/ARCHIVE/9_0_0/ncbi_cxx--9_0_0.tar.gz
+	source = LICENSE
+	md5sums = 46cbd232e024690ae617d1c44f3380b4
+	md5sums = 344b3873e649094cf2dbaac7b55cafbc
+
+pkgname = ncbi-toolkit
+
diff --git a/LICENSE b/LICENSE
new file mode 100644
index 000000000000..68c9a5485fec
--- /dev/null
+++ b/LICENSE
@@ -0,0 +1,116 @@
+CONTENTS
+
+  Public Domain Notice
+  Exceptions (for bundled 3rd-party code)
+  Copyright F.A.Q.
+
+
+
+==============================================================
+                          PUBLIC DOMAIN NOTICE
+             National Center for Biotechnology Information
+
+With the exception of certain third-party files summarized below, this
+software is a "United States Government Work" under the terms of the
+United States Copyright Act.  It was written as part of the authors'
+official duties as United States Government employees and thus cannot
+be copyrighted.  This software is freely available to the public for
+use. The National Library of Medicine and the U.S. Government have not
+placed any restriction on its use or reproduction.
+
+Although all reasonable efforts have been taken to ensure the accuracy
+and reliability of the software and data, the NLM and the U.S.
+Government do not and cannot warrant the performance or results that
+may be obtained by using this software or data. The NLM and the U.S.
+Government disclaim all warranties, express or implied, including
+warranties of performance, merchantability or fitness for any
+particular purpose.
+
+Please cite the authors in any work or product based on this material.
+
+
+
+==============================================================
+EXCEPTIONS (in all cases excluding NCBI-written makefiles):
+
+
+Location: configure
+Authors:  Free Software Foundation, Inc.
+License:  Unrestricted; at top of file
+
+Location: config.guess, config.sub
+Authors:  FSF
+License:  Unrestricted when distributed with the Toolkit;
+          standalone, GNU General Public License [gpl.txt]
+
+Location: {src,include}/dbapi/driver/ftds*/freetds
+Authors:  See src/dbapi/driver/ftds*/freetds/AUTHORS
+License:  GNU Library/Lesser General Public License
+          [src/dbapi/driver/ftds*/freetds/COPYING.LIB]
+
+Location: include/dbapi/driver/odbc/unix_odbc
+Authors:  Peter Harvey and Nick Gorham
+License:  GNU LGPL
+
+Location: {src,include}/gui/widgets/FLU
+Authors:  Jason Bryan
+License:  GNU LGPL
+
+Location: {src,include}/gui/widgets/Fl_Table
+Authors:  Greg Ercolano
+License:  GNU LGPL
+
+Location: include/util/bitset
+Author:   Anatoliy Kuznetsov
+License:  MIT [include/util/bitset/license.txt]
+
+Location: {src,include}/util/compress/bzip2
+Author:   Julian R Seward
+License:  BSDish [src/util/compress/bzip2/LICENSE]
+
+Location: {src,include}/util/compress/zlib
+Authors:  Jean-loup Gailly and Mark Adler
+License:  BSDish [include/util/compress/zlib/zlib.h]
+
+Location: {src,include}/util/regexp
+Author:   Philip Hazel
+License:  BSDish [src/util/regexp/doc/LICENCE]
+
+Location: {src,include}/misc/xmlwrapp
+Author:   Peter J Jones at al. [src/misc/xmlwrapp/AUTHORS]
+License:  BSDish [src/misc/xmlwrapp/LICENSE]
+
+
+
+==============================================================
+Copyright F.A.Q.
+
+
+--------------------------------------------------------------
+Q. Our product makes use of the NCBI source code, and we did changes
+   and additions to that version of the NCBI code to better fit it to
+   our needs. Can we copyright the code, and how?
+
+A. You can copyright only the *changes* or the *additions* you made to the
+   NCBI source code. You should identify unambiguously those sections of
+   the code that were modified, e.g. by commenting any changes you made
+   in the code you distribute. Therefore, your license has to make clear
+   to users that your product is a combination of code that is public domain
+   within the U.S. (but may be subject to copyright by the U.S. in foreign
+   countries) and code that has been created or modified by you.
+
+
+--------------------------------------------------------------
+Q. Can we (re)license all or part of the NCBI source code?
+
+A. No, you cannot license or relicense the source code written by NCBI
+   since you cannot claim any copyright in the software that was developed
+   at NCBI as a 'government work' and consequently is in the public domain
+   within the U.S.
+
+
+--------------------------------------------------------------
+Q. What if these copyright guidelines are not clear enough or are not
+   applicable to my particular case?
+
+A. Contact us. Send your questions to 'toolbox@ncbi.nlm.nih.gov'.
diff --git a/PKGBUILD b/PKGBUILD
new file mode 100644
index 000000000000..3c39c06dcdbd
--- /dev/null
+++ b/PKGBUILD
@@ -0,0 +1,48 @@
+# Maintainer: Michael Schubert <mschu.dev at gmail>
+# Contributor: Mick Elliot <micke at sfu dot ca>
+
+pkgname=ncbi-toolkit
+pkgver=9.0.0
+_pkgver=${pkgver//./_}
+pkgrel=1
+pkgdesc="Applications, scripts and C++ libraries for the analysis of biological data"
+arch=('i686' 'x86_64')
+url="http://www.ncbi.nlm.nih.gov/books/NBK7160/"
+license=('custom')
+depends=('python2' 'pcre' 'sqlite' 'lzo2' 'libtiff' 'giflib' 'libxpm' 'libmysqlclient' 'libpng' 'gnutls' 'libxml2' 'libxslt')
+optdepends=('fltk' 'wxgtk' 'db48' 'fcgi')
+makedepends=('autoconf')
+provides=('blast+-bin')
+conflicts=('blast+-bin')
+source=("ftp://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools++/ARCHIVE/$_pkgver/ncbi_cxx--$_pkgver.tar.gz" "LICENSE")
+md5sums=('46cbd232e024690ae617d1c44f3380b4'
+         '344b3873e649094cf2dbaac7b55cafbc')
+
+build()
+{
+  # for details see http://www.ncbi.nlm.nih.gov/books/NBK7167/#ch_config.Configuring_with_UNI
+  # flags that do not work: --with-dll --with-bdb
+  FLAGS="--without-debug --with-bin-release --with-bincopy --with-static \
+    --with-optimization --with-autodep --with-mt --prefix=$pkgdir/usr \
+    --libdir=$pkgdir/usr/lib --with-build-root=$srcdir/build \
+    --without-bdb --without-internal --with-optimization"
+  if [ $CARCH = "x86_64" ]; then
+    FLAGS="$FLAGS --with-64"
+  fi
+
+  cd "$srcdir/ncbi_cxx--$_pkgver"
+  ./configure $FLAGS
+
+  find src/sra/sdk -name "*.c" -exec sed -i "/curl\/types.h/d" {} \;
+
+  make
+}
+
+package() {
+  cd "$srcdir/ncbi_cxx--$_pkgver"
+
+  install -Dm644 "$srcdir/LICENSE" "$pkgdir/usr/share/licenses/$pkgname/license"
+  mv "$srcdir/build/lib/ncbi" "$pkgdir/usr/lib/" # make install error otherwise
+  make install
+}
+