academic/EMBOSS: Added (European Molecular Biology OSS)

Signed-off-by: Niels Horn <niels.horn@slackbuilds.org>

8 files changed, 154 insertions, 0 deletions

diff --git a/academic/EMBOSS/EMBOSS.SlackBuild b/academic/EMBOSS/EMBOSS.SlackBuild
new file mode 100644
index 0000000000..3ef67501d8
--- /dev/null
+++ b/academic/EMBOSS/EMBOSS.SlackBuild
@@ -0,0 +1,90 @@
+#!/bin/sh
+
+# Slackware build script for EMBOSS
+# Written by Petar Petrov, <ppetrov@paju.oulu.fi> and 
+# hereby submitted to the public domain
+
+# THIS SLACKBUILD IS DISTRIBUTETD IN THE HOPE OF BEING 
+# USEFUL BUT WITHOUT ANY WARRANTY. THE AUTHOR IS _NOT_ 
+# RESPONSIBLE FOR ANY DAMAGE OR DATA LOSS CAUSED BY IT.
+
+PRGNAM=EMBOSS			
+VERSION=${VERSION:-6.4.0}
+BUILD=${BUILD:-1}
+TAG=${TAG:-_SBo}	
+
+if [ -z "$ARCH" ]; then
+  case "$( uname -m )" in
+    i?86) ARCH=i486 ;;
+    arm*) ARCH=arm ;;
+       *) ARCH=$( uname -m ) ;;
+  esac
+fi
+
+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"
+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 . \
+ \( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \
+ -exec chmod 755 {} \; -o \
+ \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \
+ -exec chmod 644 {} \;
+
+CFLAGS="$SLKCFLAGS" \
+CXXFLAGS="$SLKCFLAGS" \
+./configure \
+  --prefix=/usr \
+  --libdir=/usr/lib${LIBDIRSUFFIX} \
+  --with-x \
+  --sysconfdir=/etc \
+  --localstatedir=/var \
+  --build=$ARCH-slackware-linux
+
+make
+make install DESTDIR=$PKG
+
+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 FAQ INSTALL NEWS README THANKS \
+  $PKG/usr/doc/$PRGNAM-$VERSION
+cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
+cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References
+
+mkdir -p $PKG/usr/share/{applications,pixmaps}
+cp $CWD/emboss.desktop $PKG/usr/share/applications
+cp $CWD/emboss.png $PKG/usr/share/pixmaps
+
+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/EMBOSS/EMBOSS.info b/academic/EMBOSS/EMBOSS.info
new file mode 100644
index 0000000000..52e4178984
--- /dev/null
+++ b/academic/EMBOSS/EMBOSS.info
@@ -0,0 +1,10 @@
+PRGNAM="EMBOSS"
+VERSION="6.4.0"
+HOMEPAGE="http://emboss.sourceforge.net/"
+DOWNLOAD="ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-6.4.0.tar.gz"
+MD5SUM="54993a22064222b01bd4fc8086f7684d"
+DOWNLOAD_x86_64=""
+MD5SUM_x86_64=""
+MAINTAINER="Petar Petrov"
+EMAIL="ppetrov@paju.oulu.fi"
+APPROVED="Niels Horn"
diff --git a/academic/EMBOSS/README b/academic/EMBOSS/README
new file mode 100644
index 0000000000..b3bb191db2
--- /dev/null
+++ b/academic/EMBOSS/README
@@ -0,0 +1,20 @@
+EMBOSS is "The European Molecular Biology Open Software Suite". 
+
+EMBOSS is a free Open Source software analysis package specially 
+developed for the needs of the molecular biology (e.g. EMBnet) user 
+community. The software automatically copes with data in a variety of 
+formats and even allows transparent retrieval of sequence data from 
+the web. Also, as extensive libraries are provided with the package, 
+it is a platform to allow other scientists to develop and release 
+software in true open source spirit. EMBOSS also integrates a range of
+currently available packages and tools for sequence analysis into a 
+seamless whole. EMBOSS breaks the historical trend towards commercial 
+software packages.
+
+For details and citation:
+EMBOSS: The European Molecular Biology Open Software Suite (2000) 
+Rice,P. Longden,I. and Bleasby,A. Trends in Genetics 16, (6) pp276-277 
+
+If you want to use eprimer3 and multiple sequence alignment programs 
+like emma, you should install primer3 and clustalw, both of which are 
+available at SlackBuilds.org.
\ No newline at end of file
diff --git a/academic/EMBOSS/References b/academic/EMBOSS/References
new file mode 100644
index 0000000000..05d39457f4
--- /dev/null
+++ b/academic/EMBOSS/References
@@ -0,0 +1,4 @@
+References
+
+EMBOSS: The European Molecular Biology Open Software Suite (2000)
+Rice,P. Longden,I. and Bleasby,A. Trends in Genetics 16, (6) pp276--277
diff --git a/academic/EMBOSS/doinst.sh b/academic/EMBOSS/doinst.sh
new file mode 100644
index 0000000000..5fb28930db
--- /dev/null
+++ b/academic/EMBOSS/doinst.sh
@@ -0,0 +1,3 @@
+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/EMBOSS/emboss.desktop b/academic/EMBOSS/emboss.desktop
new file mode 100644
index 0000000000..249650b343
--- /dev/null
+++ b/academic/EMBOSS/emboss.desktop
@@ -0,0 +1,8 @@
+[Desktop Entry]
+Categories=Education;
+Comment=Bioinformatics suite
+Exec=runJemboss.csh
+Icon=emboss.png
+Name=EMBOSS
+StartupNotify=false
+Type=Application
diff --git a/academic/EMBOSS/emboss.png b/academic/EMBOSS/emboss.png
new file mode 100644
index 0000000000..c9fd651eec
--- /dev/null
+++ b/academic/EMBOSS/emboss.png
diff --git a/academic/EMBOSS/slack-desc b/academic/EMBOSS/slack-desc
new file mode 100644
index 0000000000..ee0f082ba5
--- /dev/null
+++ b/academic/EMBOSS/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------------------------------------------------------|
+EMBOSS: EMBOSS (European Molecular Biology Open Software Suite)
+EMBOSS:
+EMBOSS: EMBOSS is a free Open Source software analysis package specially
+EMBOSS: developed for the needs of the molecular biology (e.g. EMBnet)
+EMBOSS: user community.
+EMBOSS:
+EMBOSS:
+EMBOSS:
+EMBOSS:
+EMBOSS: References: /usr/doc/EMBOSS-$VERSION/References
+EMBOSS: Home: http://emboss.sourceforge.net/