From 9855d214635ccead0b3966ce147f6f09e793735f Mon Sep 17 00:00:00 2001 From: Petar Petrov Date: Wed, 12 Sep 2012 13:51:02 -0500 Subject: academic/EMBOSS: Updated for version 6.5.7. Signed-off-by: Robby Workman --- academic/EMBOSS/EMBOSS.SlackBuild | 47 +++++++++++++++++++++++++------------- academic/EMBOSS/EMBOSS.desktop | 9 ++++++++ academic/EMBOSS/EMBOSS.info | 6 ++--- academic/EMBOSS/EMBOSS.png | Bin 0 -> 1269 bytes academic/EMBOSS/README | 41 +++++++++++++++++++++------------ academic/EMBOSS/References | 2 -- academic/EMBOSS/emboss.desktop | 8 ------- academic/EMBOSS/emboss.png | Bin 1269 -> 0 bytes academic/EMBOSS/slack-desc | 6 ++--- 9 files changed, 73 insertions(+), 46 deletions(-) create mode 100644 academic/EMBOSS/EMBOSS.desktop create mode 100644 academic/EMBOSS/EMBOSS.png delete mode 100644 academic/EMBOSS/emboss.desktop delete mode 100644 academic/EMBOSS/emboss.png (limited to 'academic/EMBOSS') 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, 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 new file mode 100644 index 0000000000..20ab180fca --- /dev/null +++ b/academic/EMBOSS/EMBOSS.desktop @@ -0,0 +1,9 @@ +[Desktop Entry] +Categories=Education; +Comment=Bioinformatics suite +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 new file mode 100644 index 0000000000..c9fd651eec Binary files /dev/null and b/academic/EMBOSS/EMBOSS.png 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/emboss.desktop b/academic/EMBOSS/emboss.desktop deleted file mode 100644 index 249650b343..0000000000 --- a/academic/EMBOSS/emboss.desktop +++ /dev/null @@ -1,8 +0,0 @@ -[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 deleted file mode 100644 index c9fd651eec..0000000000 Binary files a/academic/EMBOSS/emboss.png and /dev/null differ 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: -- cgit v1.2.3