academic/bpp1.9-utils: Added (Bio++ 1.9 Utils Library)

Signed-off-by: Dave Woodfall <dave@slackbuilds.org>

Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>

4 files changed, 153 insertions, 0 deletions

diff --git a/academic/bpp1.9-utils/README b/academic/bpp1.9-utils/README
new file mode 100644
index 0000000000000..5ee42d96328b0
--- /dev/null
+++ b/academic/bpp1.9-utils/README
@@ -0,0 +1,10 @@
+Bio++ is a set of C++ libraries for Bioinformatics, including sequence
+analysis, phylogenetics, molecular evolution and population genetics.
+Bio++ is Object Oriented and is designed to be both easy to use and
+computer efficient. Bio++ intends to help programmers to write
+computer expensive programs, by providing them a set of re-usable
+tools.
+
+This contains the Bio++ 1.9 (April 2010) Utils Library. It can be
+installed along the current Bio++ suite libraries, however they better
+not be present at compile time.
diff --git a/academic/bpp1.9-utils/bpp1.9-utils.SlackBuild b/academic/bpp1.9-utils/bpp1.9-utils.SlackBuild
new file mode 100644
index 0000000000000..daff8c88bf5de
--- /dev/null
+++ b/academic/bpp1.9-utils/bpp1.9-utils.SlackBuild
@@ -0,0 +1,114 @@
+#!/bin/sh
+
+# Slackware build script for bpp1.9-utils
+
+# Copyright 2020 Petar Petrov slackalaxy@gmail.com
+# All rights reserved.
+#
+# Redistribution and use of this script, with or without modification, is
+# permitted provided that the following conditions are met:
+#
+# 1. Redistributions of this script must retain the above copyright
+#    notice, this list of conditions and the following disclaimer.
+#
+#  THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED
+#  WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
+#  MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.  IN NO
+#  EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+#  SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+#  PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+#  OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+#  WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+#  OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+#  ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+PRGNAM=bpp1.9-utils
+SRCNAM=bpp-utils
+VERSION=${VERSION:-1.5.0}
+BUILD=${BUILD:-1}
+TAG=${TAG:-_SBo}
+
+if [ -z "$ARCH" ]; then
+  case "$( uname -m )" in
+    i?86) ARCH=i586 ;;
+    arm*) ARCH=arm ;;
+       *) ARCH=$( uname -m ) ;;
+  esac
+fi
+
+CWD=$(pwd)
+TMP=${TMP:-/tmp/SBo}
+PKG=$TMP/package-$PRGNAM
+OUTPUT=${OUTPUT:-/tmp}
+
+if [ "$ARCH" = "i586" ]; then
+  SLKCFLAGS="-O2 -march=i586 -mtune=i686"
+  LIBDIRSUFFIX=""
+elif [ "$ARCH" = "i686" ]; then
+  SLKCFLAGS="-O2 -march=i686 -mtune=i686"
+  LIBDIRSUFFIX=""
+elif [ "$ARCH" = "x86_64" ]; then
+  SLKCFLAGS="-O2 -fPIC"
+  LIBDIRSUFFIX="64"
+else
+  SLKCFLAGS="-O2"
+  LIBDIRSUFFIX=""
+fi
+
+# This is needed for vCAPS to find its libraries at runtime. Thanks Urachlay!
+LIBDIRPATH="-Wl,-rpath,/usr/lib${LIBDIRSUFFIX}/Bpp1.9"
+
+set -e
+
+rm -rf $PKG
+mkdir -p $TMP $PKG $OUTPUT
+cd $TMP
+rm -rf $SRCNAM-$VERSION
+tar xvf $CWD/$SRCNAM-$VERSION.tar.gz
+cd $SRCNAM-$VERSION
+chown -R root:root .
+find -L . \
+ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \
+  -o -perm 511 \) -exec chmod 755 {} \; -o \
+ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \
+  -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \;
+
+# This is needed on newer systems (-current)
+sed -i "s:file;:file.good();:g" Utils/FileTools.cpp
+
+# Use custom install place, so libs can coexist with latest Bio++
+sed -i "s:/lib/:/lib${LIBDIRSUFFIX}/Bpp1.9/:g" Utils.spec
+
+mkdir -p build
+cd build
+  cmake \
+    -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS $LIBDIRPATH" \
+    -DCMAKE_INSTALL_PREFIX=/usr \
+    -DCMAKE_BUILD_TYPE=Release ..
+
+# More about word boundary and sed:
+# https://linuxize.com/post/how-to-use-sed-to-find-and-replace-string-in-files/
+sed -i "s:/lib/:/lib${LIBDIRSUFFIX}/Bpp1.9/:g" Utils/cmake_install.cmake
+sed -i "s:/lib\b:/lib${LIBDIRSUFFIX}/Bpp1.9:g" Utils/cmake_install.cmake
+
+  make
+  make DESTDIR=$PKG install
+cd ..
+
+# static library not needed
+rm -f $PKG/usr/lib$LIBDIRSUFFIX/Bpp1.9/libbpp-utils.a
+
+find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \
+  | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true
+
+mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
+cp -a \
+  AUTHORS ChangeLog COPYING INSTALL \
+  $PKG/usr/doc/$PRGNAM-$VERSION
+cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
+
+mkdir -p $PKG/install
+cat $CWD/slack-desc > $PKG/install/slack-desc
+
+cd $PKG
+/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz}
diff --git a/academic/bpp1.9-utils/bpp1.9-utils.info b/academic/bpp1.9-utils/bpp1.9-utils.info
new file mode 100644
index 0000000000000..8e7863e9f11cf
--- /dev/null
+++ b/academic/bpp1.9-utils/bpp1.9-utils.info
@@ -0,0 +1,10 @@
+PRGNAM="bpp1.9-utils"
+VERSION="1.5.0"
+HOMEPAGE="http://biopp.univ-montp2.fr/"
+DOWNLOAD="http://biopp.univ-montp2.fr/repos/sources/bpp-utils-1.5.0.tar.gz"
+MD5SUM="4625b7f2146caa1815ed7dc433d5eb78"
+DOWNLOAD_x86_64=""
+MD5SUM_x86_64=""
+REQUIRES=""
+MAINTAINER="Petar Petrov"
+EMAIL="slackalaxy@gmail.copm"
diff --git a/academic/bpp1.9-utils/slack-desc b/academic/bpp1.9-utils/slack-desc
new file mode 100644
index 0000000000000..be9d333c61fa9
--- /dev/null
+++ b/academic/bpp1.9-utils/slack-desc
@@ -0,0 +1,19 @@
+# HOW TO EDIT THIS FILE:
+# The "handy ruler" below makes it easier to edit a package description.
+# Line up the first '|' above the ':' following the base package name, and
+# the '|' on the right side marks the last column you can put a character in.
+# You must make exactly 11 lines for the formatting to be correct.  It's also
+# customary to leave one space after the ':' except on otherwise blank lines.
+
+            |-----handy-ruler------------------------------------------------------|
+bpp1.9-utils: bpp1.9-utils (Bio++ 1.9 Utils Library)
+bpp1.9-utils:
+bpp1.9-utils: Contains the Bio++ 1.9 Utils Library.
+bpp1.9-utils:
+bpp1.9-utils:
+bpp1.9-utils:
+bpp1.9-utils:
+bpp1.9-utils:
+bpp1.9-utils:
+bpp1.9-utils:
+bpp1.9-utils: