academic/SeqMonk: Added (A Mapped Sequence Analysis tool)
Signed-off-by: Dave Woodfall <dave@slackbuilds.org> Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>
This commit is contained in:
Petar Petrov
Willy Sudiarto Raharjo
parent
21c3c2f497
commit
8a25ffde0f
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SeqMonk - A Mapped Sequence Analysis tool
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-----------------------------------------
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SeqMonk is a tool for viewing and analysing mapped sequence data. It
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was initially written to cope with remapping experiment data from
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next generation sequencers, but could be applied to any dataset
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consisting of a series of mapped genomic regions. The program allows
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you to visualise the positions of your mapped regions against an
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annotated genome and to quantify the data in order to make comparisons
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between data sets.
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If you have any comments about SeqMonk the authors would like to hear
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them. You either enter them in the bug tracking system at:
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https://github.com/s-andrews/seqmonk/issues/
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#!/bin/sh
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# Slackware build script for SeqMonk
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# Copyright 2020 Petar Petrov slackalaxy@gmail.com
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# All rights reserved.
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#
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# Redistribution and use of this script, with or without modification, is
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# permitted provided that the following conditions are met:
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#
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# 1. Redistributions of this script must retain the above copyright
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# notice, this list of conditions and the following disclaimer.
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#
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# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED
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# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
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# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO
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# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
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# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
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# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
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# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
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# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
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# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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PRGNAM=SeqMonk
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VERSION=${VERSION:-1.47.1}
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BUILD=${BUILD:-1}
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TAG=${TAG:-_SBo}
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EXENAM=seqmonk
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TARNAM=${EXENAM}_v${VERSION}_linux64
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if [ -z "$ARCH" ]; then
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case "$( uname -m )" in
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i?86) ARCH=i586 ;;
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arm*) ARCH=arm ;;
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*) ARCH=$( uname -m ) ;;
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esac
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fi
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CWD=$(pwd)
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TMP=${TMP:-/tmp/SBo}
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PKG=$TMP/package-$PRGNAM
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OUTPUT=${OUTPUT:-/tmp}
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if [ "$ARCH" = "i586" ]; then
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SLKCFLAGS="-O2 -march=i586 -mtune=i686"
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LIBDIRSUFFIX=""
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elif [ "$ARCH" = "i686" ]; then
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SLKCFLAGS="-O2 -march=i686 -mtune=i686"
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LIBDIRSUFFIX=""
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elif [ "$ARCH" = "x86_64" ]; then
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SLKCFLAGS="-O2 -fPIC"
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LIBDIRSUFFIX="64"
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else
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SLKCFLAGS="-O2"
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LIBDIRSUFFIX=""
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fi
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set -e
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if [ "$ARCH" != "x86_64" ]; then
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printf "\n\n$ARCH is not supported... \n"
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exit 1
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fi
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rm -rf $PKG
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mkdir -p $TMP $PKG $OUTPUT
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cd $TMP
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rm -rf $PRGNAM
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tar xvf $CWD/$TARNAM.tar.gz
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cd $PRGNAM
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chown -R root:root .
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find -L . \
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\( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \
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-o -perm 511 \) -exec chmod 755 {} \; -o \
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\( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \
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-o -perm 440 -o -perm 400 \) -exec chmod 644 {} \;
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# Make sure SeqMonk finds its own java environment
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sed -i 's:java -version:$RealBin/jre/bin/java -version:' seqmonk
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# Change icon path and category in the desktop file
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sed -i "s:/usr/local/SeqMonk/uk/ac/bbsrc/babraham/SeqMonk/Resources/monk.svg:$EXENAM:" $EXENAM.desktop
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sed -i "s:Categories=Application:Categories=Education:" $EXENAM.desktop
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mkdir -p $PKG/opt/$PRGNAM
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cp -a \
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com edu Help jre net Scripts Templates uk *.jar seqmonk seqmonk_import \
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$PKG/opt/$PRGNAM
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mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
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cp -a \
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INSTALL.txt LICENSE LICENSE.txt NOTICE_FOR_COMMONS_MATH_CODE.txt README.md README.txt RELEASE_NOTES.txt \
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$PKG/usr/doc/$PRGNAM-$VERSION
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cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
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mkdir -p $PKG/usr/share/{applications,pixmaps}
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cp -a uk/ac/babraham/SeqMonk/Resources/monk_logo.png $PKG/usr/share/pixmaps/$EXENAM.png
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cp -a $EXENAM.desktop $PKG/usr/share/applications
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# Leave the program in /opt and create a symlink to it
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mkdir -p $PKG/usr/bin
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cd $PKG/usr/bin
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ln -s ../../opt/$PRGNAM/$EXENAM .
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cd -
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mkdir -p $PKG/install
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cat $CWD/slack-desc > $PKG/install/slack-desc
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cat $CWD/doinst.sh > $PKG/install/doinst.sh
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cd $PKG
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/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz}
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@ -0,0 +1,10 @@
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PRGNAM="SeqMonk"
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VERSION="1.47.1"
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HOMEPAGE="https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/"
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DOWNLOAD="UNSUPPORTED"
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MD5SUM=""
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DOWNLOAD_x86_64="https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/seqmonk_v1.47.1_linux64.tar.gz"
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MD5SUM_x86_64="e7c80b113e4c80d26e7eca468a636134"
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REQUIRES="R"
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MAINTAINER="Petar Petrov"
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EMAIL="slackalaxy@gmail.com"
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@ -0,0 +1,3 @@
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if [ -x /usr/bin/update-desktop-database ]; then
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/usr/bin/update-desktop-database -q usr/share/applications >/dev/null 2>&1
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fi
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@ -0,0 +1,19 @@
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# HOW TO EDIT THIS FILE:
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# The "handy ruler" below makes it easier to edit a package description.
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# Line up the first '|' above the ':' following the base package name, and
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# the '|' on the right side marks the last column you can put a character in.
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# You must make exactly 11 lines for the formatting to be correct. It's also
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# customary to leave one space after the ':' except on otherwise blank lines.
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|-----handy-ruler------------------------------------------------------|
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SeqMonk: SeqMonk (A Mapped Sequence Analysis tool)
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SeqMonk:
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SeqMonk: SeqMonk is a tool for viewing and analysing mapped sequence data.
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SeqMonk: It was initially written to cope with remapping experiment data
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SeqMonk: from next generation sequencers, but could be applied to any
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SeqMonk: dataset consisting of a series of mapped genomic regions. The
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SeqMonk: program allows you to visualise the positions of your mapped
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SeqMonk: regions against an annotated genome and to quantify the data in
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SeqMonk: order to make comparisons between data sets.
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SeqMonk:
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SeqMonk: https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/
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