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-rw-r--r--academic/EMBOSS/EMBOSS.SlackBuild47
-rw-r--r--academic/EMBOSS/EMBOSS.desktop (renamed from academic/EMBOSS/emboss.desktop)5
-rw-r--r--academic/EMBOSS/EMBOSS.info6
-rw-r--r--academic/EMBOSS/EMBOSS.png (renamed from academic/EMBOSS/emboss.png)bin1269 -> 1269 bytes
-rw-r--r--academic/EMBOSS/README41
-rw-r--r--academic/EMBOSS/References2
-rw-r--r--academic/EMBOSS/slack-desc6
7 files changed, 67 insertions, 40 deletions
diff --git a/academic/EMBOSS/EMBOSS.SlackBuild b/academic/EMBOSS/EMBOSS.SlackBuild
index 0321ba1146..7c18b5d7d2 100644
--- a/academic/EMBOSS/EMBOSS.SlackBuild
+++ b/academic/EMBOSS/EMBOSS.SlackBuild
@@ -1,17 +1,31 @@
#!/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:-3}
-TAG=${TAG:-_SBo}
+# Copyright 2011-2012 Petar Petrov, ppetrov@paju.oulu.fi
+# All rights reserved.
+#
+# Redistribution and use of this script, with or without modification, is
+# permitted provided that the following conditions are met:
+#
+# 1. Redistributions of this script must retain the above copyright
+# notice, this list of conditions and the following disclaimer.
+#
+# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED
+# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
+# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO
+# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE
+
+PRGNAM=EMBOSS
+VERSION=${VERSION:-6.5.7}
+BUILD=${BUILD:-1}
+TAG=${TAG:-_SBo}
if [ -z "$ARCH" ]; then
case "$( uname -m )" in
@@ -49,9 +63,6 @@ rm -rf $PRGNAM-$VERSION
tar xvf $CWD/$PRGNAM-$VERSION.tar.gz
cd $PRGNAM-$VERSION
-# Apply EMBOSS bug-fix set 1-24. Thanks to Alan at ajb@ebi.ac.uk!
-patch -p1 < $CWD/patch-1-24
-
chown -R root:root .
find . \
\( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \
@@ -59,6 +70,9 @@ find . \
\( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \
-exec chmod 644 {} \;
+# We do not need to check for EMBOSS updates
+sed -i "/embossupdate/d" Makefile.am Makefile.in
+
CFLAGS="$SLKCFLAGS" \
CXXFLAGS="$SLKCFLAGS" \
./configure \
@@ -67,6 +81,7 @@ CXXFLAGS="$SLKCFLAGS" \
--with-x \
--sysconfdir=/etc \
--localstatedir=/var \
+ --docdir=/usr/doc/$PRGNAM-$VERSION \
--build=$ARCH-slackware-linux
make
@@ -77,14 +92,14 @@ find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | gr
mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
cp -a \
- AUTHORS ChangeLog COPYING FAQ INSTALL NEWS README THANKS \
+ AUTHORS ChangeLog COPYING FAQ INSTALL LICENSE 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
+cp $CWD/$PRGNAM.desktop $PKG/usr/share/applications
+cp $CWD/$PRGNAM.png $PKG/usr/share/pixmaps
mkdir -p $PKG/install
cat $CWD/slack-desc > $PKG/install/slack-desc
diff --git a/academic/EMBOSS/emboss.desktop b/academic/EMBOSS/EMBOSS.desktop
index 249650b343..20ab180fca 100644
--- a/academic/EMBOSS/emboss.desktop
+++ b/academic/EMBOSS/EMBOSS.desktop
@@ -1,8 +1,9 @@
[Desktop Entry]
Categories=Education;
Comment=Bioinformatics suite
-Exec=runJemboss.csh
-Icon=emboss.png
+Exec=runJemboss.sh
+Icon=EMBOSS.png
Name=EMBOSS
StartupNotify=false
Type=Application
+GenericName=
diff --git a/academic/EMBOSS/EMBOSS.info b/academic/EMBOSS/EMBOSS.info
index ec6b3e7464..559c221334 100644
--- a/academic/EMBOSS/EMBOSS.info
+++ b/academic/EMBOSS/EMBOSS.info
@@ -1,8 +1,8 @@
PRGNAM="EMBOSS"
-VERSION="6.4.0"
+VERSION="6.5.7"
HOMEPAGE="http://emboss.sourceforge.net/"
-DOWNLOAD="ftp://emboss.open-bio.org/pub/EMBOSS/old/6.4.0/EMBOSS-6.4.0.tar.gz"
-MD5SUM="54993a22064222b01bd4fc8086f7684d"
+DOWNLOAD="ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-6.5.7.tar.gz"
+MD5SUM="6a2cb3f93d5e9415c74ab0f6b1ede5f0"
DOWNLOAD_x86_64=""
MD5SUM_x86_64=""
REQUIRES="jdk"
diff --git a/academic/EMBOSS/emboss.png b/academic/EMBOSS/EMBOSS.png
index c9fd651eec..c9fd651eec 100644
--- a/academic/EMBOSS/emboss.png
+++ b/academic/EMBOSS/EMBOSS.png
Binary files differ
diff --git a/academic/EMBOSS/README b/academic/EMBOSS/README
index 7c74ec3bc8..c45a7fe0ad 100644
--- a/academic/EMBOSS/README
+++ b/academic/EMBOSS/README
@@ -1,19 +1,32 @@
-EMBOSS is "The European Molecular Biology Open Software Suite".
+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
+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
+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
+Within EMBOSS you will find around hundreds of programs (applications)
+covering areas such as:
+
+- Sequence alignment
+- Rapid database searching with sequence patterns
+- Protein motif identification, including domain analysis
+- Nucleotide sequence pattern analysis -- for example to identify CpG
+ islands or repeats
+- Codon usage analysis for small genomes
+- Rapid identification of sequence patterns in large scale sequence
+ sets
+- Presentation tools for publication
-If you want to use eprimer3 and multiple sequence alignment programs
-like emma, you should install primer3 and clustalw.
+Optional, run-time dependencies are clustalw and primer3 -- needed if
+you want to use the wrappers emma and eprimer32.
+
+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
diff --git a/academic/EMBOSS/References b/academic/EMBOSS/References
index 05d39457f4..975a98e59c 100644
--- a/academic/EMBOSS/References
+++ b/academic/EMBOSS/References
@@ -1,4 +1,2 @@
-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/slack-desc b/academic/EMBOSS/slack-desc
index ee0f082ba5..0f45f61c86 100644
--- a/academic/EMBOSS/slack-desc
+++ b/academic/EMBOSS/slack-desc
@@ -12,8 +12,8 @@ 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: Details: /usr/share/EMBOSS/doc
EMBOSS: Home: http://emboss.sourceforge.net/
+EMBOSS:
+EMBOSS: