academic/avogadro: Added to 13.0 repository

6 files changed, 156 insertions, 0 deletions

diff --git a/academic/avogadro/README b/academic/avogadro/README
new file mode 100644
index 0000000000000..cc86a06205b19
--- /dev/null
+++ b/academic/avogadro/README
@@ -0,0 +1,5 @@
+Avogadro is a molecular graphics and modelling system targeted at molecules 
+and biomolecules. It can visualize properties like molecular orbitals or 
+electrostatic potentials and features an intuitive molecular builder.
+
+This requires openbabel and numpy.
diff --git a/academic/avogadro/avogadro.1 b/academic/avogadro/avogadro.1
new file mode 100644
index 0000000000000..1d0be42620e9c
--- /dev/null
+++ b/academic/avogadro/avogadro.1
@@ -0,0 +1,29 @@
+.TH "AVOGADRO" "1" "22 January 2009" "" "User commands"
+
+.SH NAME
+avogadro \- Molecular Graphics and Modelling System
+
+.SH SYNOPSIS
+\fBavogadro\fR [\fBoptions\fR] [\fIfiles\fR]
+
+.SH DESCRIPTION
+.PP
+\fBavogadro\fR is a molecular graphics and modelling system targeted at molecules
+and biomolecules.  It can visualize properties like molecular orbitals or
+electrostatic potentials and features an intuitive molecular builder.
+
+.SH OPTIONS
+.PP
+Listed below are the command line options for \fBavogadro\fR:
+.TP
+.B \-\-help, \-h
+Show help options.
+.TP
+.B \-\-version, \-v
+Show version information.
+
+.SH AUTHOR
+.PP
+This manual page was written by Jordan Mantha <\&laserjock@ubuntu.com\&>.
+.PP
+Released under the GNU General Public License, version 2 or later.
diff --git a/academic/avogadro/avogadro.SlackBuild b/academic/avogadro/avogadro.SlackBuild
new file mode 100644
index 0000000000000..35665408e5ecb
--- /dev/null
+++ b/academic/avogadro/avogadro.SlackBuild
@@ -0,0 +1,89 @@
+#!/bin/sh
+
+# Slackware build script for Avogadro
+
+# Written by Larry Hajali <larryhaja[at]gmail[dot]com>
+
+PRGNAM=avogadro
+VERSION=${VERSION:-0.9.7}
+ARCH=${ARCH:-i486}
+BUILD=${BUILD:-1}
+TAG=${TAG:-_SBo}
+
+CWD=$(pwd)
+TMP=${TMP:-/tmp/SBo}
+PKG=$TMP/package-$PRGNAM
+OUTPUT=${OUTPUT:-/tmp}
+
+if [ "$ARCH" = "i486" ]; then
+  SLKCFLAGS="-O2 -march=i486 -mtune=i686"
+  LIBDIRSUFFIX=""
+elif [ "$ARCH" = "i686" ]; then
+  SLKCFLAGS="-O2 -march=i686 -mtune=i686"
+  LIBDIRSUFFIX=""
+elif [ "$ARCH" = "x86_64" ]; then
+  SLKCFLAGS="-O2 -fPIC"
+  LIBDIRSUFFIX="64"
+fi
+
+set -e
+
+rm -rf $PKG
+mkdir -p $TMP $PKG $OUTPUT
+cd $TMP
+rm -rf $PRGNAM-$VERSION
+tar xvf $CWD/$PRGNAM-$VERSION.tar.bz2
+cd $PRGNAM-$VERSION
+chown -R root:root .
+find . \
+ \( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \
+ -exec chmod 755 {} \; -o \
+ \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \
+ -exec chmod 644 {} \;
+
+# Fix icon name in desktop menu item.
+sed -i '/^Icon/s|=.*|=avogadro-icon.png|' avogadro/src/avogadro.desktop
+
+mkdir build && cd build
+  cmake \
+    -DCMAKE_INSTALL_PREFIX=/usr \
+    -DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \
+    -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \
+    -DLIB_SUFFIX=${LIBDIRSUFFIX} \
+    -DENABLE_RPATH=OFF \
+    -DCMAKE_SKIP_RPATH=YES \
+    -DENABLE_GLSL=ON \
+    -DENABLE_UPDATE_CHECKER=OFF \
+    -DCMAKE_BUILD_TYPE=Release ..
+
+  make VERBOSE=1
+  make install DESTDIR=$PKG
+cd -
+
+# Remove file to prevent avogadro from segfaulting.
+#rm -f $PKG/usr/share/libavogadro/extensionScripts/example.py
+
+( cd $PKG
+  find . | xargs file | grep "executable" | grep ELF | cut -f 1 -d : | \
+    xargs strip --strip-unneeded 2> /dev/null || true
+  find . | xargs file | grep "shared object" | grep ELF | cut -f 1 -d : | \
+    xargs strip --strip-unneeded 2> /dev/null
+)
+
+mkdir -p $PKG/usr/man/man1
+install -m 0644 $CWD/$PRGNAM.1 $PKG/usr/man/man1/
+gzip -9 $PKG/usr/man/man?/*.?
+
+mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
+cp -a \
+  AUTHORS ChangeLog COPYING INSTALL cmake/modules/COPYING-CMAKE-SCRIPTS \
+  avogadro/gl2ps/{COPYING*,TODO} \
+  $PKG/usr/doc/$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
+cat $CWD/doinst.sh > $PKG/install/doinst.sh
+
+cd $PKG
+/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz}
diff --git a/academic/avogadro/avogadro.info b/academic/avogadro/avogadro.info
new file mode 100644
index 0000000000000..f37956de143bf
--- /dev/null
+++ b/academic/avogadro/avogadro.info
@@ -0,0 +1,10 @@
+PRGNAM="avogadro"
+VERSION="0.9.7"
+HOMEPAGE="http://avogadro.openmolecules.net/wiki/Main_Page"
+DOWNLOAD="http://downloads.sourceforge.net/avogadro/avogadro-0.9.7.tar.bz2"
+MD5SUM="13234be4e2caa6017721b937a276cdd9"
+DOWNLOAD_x86_64=""
+MD5SUM_x86_64=""
+MAINTAINER="Larry Hajali"
+EMAIL="larryhaja[at]gmail[dot]com"
+APPROVED="rworkman"
diff --git a/academic/avogadro/doinst.sh b/academic/avogadro/doinst.sh
new file mode 100644
index 0000000000000..4e8ba7071dea7
--- /dev/null
+++ b/academic/avogadro/doinst.sh
@@ -0,0 +1,4 @@
+if [ -x /usr/bin/update-desktop-database ]; then
+  /usr/bin/update-desktop-database -q usr/share/applications >/dev/null 2>&1
+fi
+
diff --git a/academic/avogadro/slack-desc b/academic/avogadro/slack-desc
new file mode 100644
index 0000000000000..bda77bc1762fd
--- /dev/null
+++ b/academic/avogadro/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 ':'.
+
+        |-----handy-ruler------------------------------------------------------|
+avogadro: Avogadro (An advanced molecular editor based on Qt 4.)
+avogadro:
+avogadro: Avogadro is a molecular graphics and modelling system targetted at
+avogadro: molecules and biomolecules. It can visualize properties like
+avogadro: molecular orbitals or electrostatic potentials and features an
+avogadro: intuitive molecular builder.
+avogadro:
+avogadro: Homepage: http://avogadro.openmolecules.net/wiki/Main_Page
+avogadro:
+avogadro:
+avogadro: