academic/bppsuite: Added (Bio++ program suite)

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

4 files changed, 153 insertions, 0 deletions

diff --git a/academic/bppsuite/README b/academic/bppsuite/README
new file mode 100644
index 000000000000..cc877ea40b0a
--- /dev/null
+++ b/academic/bppsuite/README
@@ -0,0 +1,11 @@
+Bio++ program suite
+
+The Bio++ Program Suite is a package of programs using the Bio++
+libraries and dedicated to Phylogenetics and Molecular Evolution. All
+programs are independent, but can be combined to perform rather
+complex analyses. These programs use the interface helper tools of the
+libraries, and hence share the same syntax. They also have several
+options in common, which may also be shared by third-party software.
+
+Detailed documentation can be found (as PDF and HTML) here:
+https://github.com/BioPP/bppsuite/releases/tag/v2.3.2
diff --git a/academic/bppsuite/bppsuite.SlackBuild b/academic/bppsuite/bppsuite.SlackBuild
new file mode 100644
index 000000000000..4e4bc8c2d2ba
--- /dev/null
+++ b/academic/bppsuite/bppsuite.SlackBuild
@@ -0,0 +1,113 @@
+#!/bin/bash
+
+# Slackware build script for bppsuite
+
+# Copyright 2017-2022 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.
+
+cd $(dirname $0) ; CWD=$(pwd)
+
+PRGNAM=bppsuite
+VERSION=${VERSION:-2.4.1}
+BUILD=${BUILD:-1}
+TAG=${TAG:-_SBo}
+PKGTYPE=${PKGTYPE:-tgz}
+
+if [ -z "$ARCH" ]; then
+  case "$( uname -m )" in
+    i?86) ARCH=i586 ;;
+    arm*) ARCH=arm ;;
+       *) ARCH=$( uname -m ) ;;
+  esac
+fi
+
+if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then
+  echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE"
+  exit 0
+fi
+
+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
+
+set -e
+
+rm -rf $PKG
+mkdir -p $TMP $PKG $OUTPUT
+cd $TMP
+rm -rf $PRGNAM-$VERSION
+tar xvf $CWD/$PRGNAM-$VERSION.tar.gz
+cd $PRGNAM-$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 {} \;
+
+mkdir -p build
+cd build
+  cmake \
+    -DCMAKE_FLAGS:STRING="$SLKCFLAGS" \
+    -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \
+    -DCMAKE_INSTALL_PREFIX=/usr \
+    -DCMAKE_BUILD_TYPE=Release ..
+  make
+  make install DESTDIR=$PKG
+cd ..
+
+# Place man pages to their proper location
+mkdir -p $PKG/usr/man/man1
+mv $PKG/usr/share/man/man1/* $PKG/usr/man/man1
+
+# Place info pages to their proper location
+mkdir -p $PKG/usr/info
+mv $PKG/usr/share/info/* $PKG/usr/info
+rm -rf $PKG/usr/share
+
+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
+
+rm -f $PKG/usr/info/dir
+gzip -9 $PKG/usr/info/*.info*
+
+mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
+cp -a AUTHORS.txt ChangeLog COPYING.txt README.md $PKG/usr/doc/$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
diff --git a/academic/bppsuite/bppsuite.info b/academic/bppsuite/bppsuite.info
new file mode 100644
index 000000000000..97626a2bff0c
--- /dev/null
+++ b/academic/bppsuite/bppsuite.info
@@ -0,0 +1,10 @@
+PRGNAM="bppsuite"
+VERSION="2.4.1"
+HOMEPAGE="https://github.com/BioPP/"
+DOWNLOAD="https://github.com/BioPP/bppsuite/archive/v2.4.1/bppsuite-2.4.1.tar.gz"
+MD5SUM="d254ffd9e121b408aed36f49e62920d1"
+DOWNLOAD_x86_64=""
+MD5SUM_x86_64=""
+REQUIRES="bpp-seq-omics bpp-phyl-omics bpp-popgen"
+MAINTAINER="Petar Petrov"
+EMAIL="slackalaxy@gmail.com"
diff --git a/academic/bppsuite/slack-desc b/academic/bppsuite/slack-desc
new file mode 100644
index 000000000000..8419aa4f1e79
--- /dev/null
+++ b/academic/bppsuite/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------------------------------------------------------|
+bppsuite: bppsuite (Bio++ program suite)
+bppsuite:
+bppsuite: The Bio++ Program Suite is a package of programs using the Bio++
+bppsuite: libraries and dedicated to Phylogenetics and Molecular Evolution.
+bppsuite: All programs are independent, but can be combined to perform
+bppsuite: rather complex analyses. These programs use the interface helper
+bppsuite: tools of the libraries, and hence share the same syntax. They also
+bppsuite: have several options in common, which may also be shared by third-
+bppsuite: party software.
+bppsuite:
+bppsuite: Git: https://github.com/BioPP/bppsuite