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author | 2020-10-30 21:05:50 +0000 | |
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committer | 2020-10-31 11:15:27 +0700 | |
commit | 8a25ffde0f7aad2c7449afd83dcd4d2c300aa504 (patch) | |
tree | 9cc17a093ef117730d5b1cd5cdd1515ecbd5db05 /academic/SeqMonk | |
parent | 21c3c2f49763394faf9ce74dfdf2818b547daa01 (diff) | |
download | slackbuilds-8a25ffde0f7aad2c7449afd83dcd4d2c300aa504.tar.gz slackbuilds-8a25ffde0f7aad2c7449afd83dcd4d2c300aa504.tar.xz |
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>
Diffstat (limited to 'academic/SeqMonk')
-rw-r--r-- | academic/SeqMonk/README | 15 | ||||
-rw-r--r-- | academic/SeqMonk/SeqMonk.SlackBuild | 113 | ||||
-rw-r--r-- | academic/SeqMonk/SeqMonk.info | 10 | ||||
-rw-r--r-- | academic/SeqMonk/doinst.sh | 3 | ||||
-rw-r--r-- | academic/SeqMonk/slack-desc | 19 |
5 files changed, 160 insertions, 0 deletions
diff --git a/academic/SeqMonk/README b/academic/SeqMonk/README new file mode 100644 index 0000000000..a5d7990f84 --- /dev/null +++ b/academic/SeqMonk/README @@ -0,0 +1,15 @@ +SeqMonk - A Mapped Sequence Analysis tool +----------------------------------------- + +SeqMonk is a tool for viewing and analysing mapped sequence data. It +was initially written to cope with remapping experiment data from +next generation sequencers, but could be applied to any dataset +consisting of a series of mapped genomic regions. The program allows +you to visualise the positions of your mapped regions against an +annotated genome and to quantify the data in order to make comparisons +between data sets. + +If you have any comments about SeqMonk the authors would like to hear +them. You either enter them in the bug tracking system at: + +https://github.com/s-andrews/seqmonk/issues/ diff --git a/academic/SeqMonk/SeqMonk.SlackBuild b/academic/SeqMonk/SeqMonk.SlackBuild new file mode 100644 index 0000000000..e09ee60c9a --- /dev/null +++ b/academic/SeqMonk/SeqMonk.SlackBuild @@ -0,0 +1,113 @@ +#!/bin/sh + +# Slackware build script for SeqMonk + +# Copyright 2020 Petar Petrov slackalaxy@gmail.com +# 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=SeqMonk +VERSION=${VERSION:-1.47.1} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +EXENAM=seqmonk +TARNAM=${EXENAM}_v${VERSION}_linux64 + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +CWD=$(pwd) +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -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 + +if [ "$ARCH" != "x86_64" ]; then + printf "\n\n$ARCH is not supported... \n" + exit 1 +fi + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM +tar xvf $CWD/$TARNAM.tar.gz +cd $PRGNAM +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +# Make sure SeqMonk finds its own java environment +sed -i 's:java -version:$RealBin/jre/bin/java -version:' seqmonk + +# Change icon path and category in the desktop file +sed -i "s:/usr/local/SeqMonk/uk/ac/bbsrc/babraham/SeqMonk/Resources/monk.svg:$EXENAM:" $EXENAM.desktop +sed -i "s:Categories=Application:Categories=Education:" $EXENAM.desktop + +mkdir -p $PKG/opt/$PRGNAM +cp -a \ + com edu Help jre net Scripts Templates uk *.jar seqmonk seqmonk_import \ + $PKG/opt/$PRGNAM + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + INSTALL.txt LICENSE LICENSE.txt NOTICE_FOR_COMMONS_MATH_CODE.txt README.md README.txt RELEASE_NOTES.txt \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/usr/share/{applications,pixmaps} +cp -a uk/ac/babraham/SeqMonk/Resources/monk_logo.png $PKG/usr/share/pixmaps/$EXENAM.png +cp -a $EXENAM.desktop $PKG/usr/share/applications + +# Leave the program in /opt and create a symlink to it +mkdir -p $PKG/usr/bin +cd $PKG/usr/bin +ln -s ../../opt/$PRGNAM/$EXENAM . +cd - + +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/SeqMonk/SeqMonk.info b/academic/SeqMonk/SeqMonk.info new file mode 100644 index 0000000000..af8b37178c --- /dev/null +++ b/academic/SeqMonk/SeqMonk.info @@ -0,0 +1,10 @@ +PRGNAM="SeqMonk" +VERSION="1.47.1" +HOMEPAGE="https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/" +DOWNLOAD="UNSUPPORTED" +MD5SUM="" +DOWNLOAD_x86_64="https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/seqmonk_v1.47.1_linux64.tar.gz" +MD5SUM_x86_64="e7c80b113e4c80d26e7eca468a636134" +REQUIRES="R" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/SeqMonk/doinst.sh b/academic/SeqMonk/doinst.sh new file mode 100644 index 0000000000..5fb28930db --- /dev/null +++ b/academic/SeqMonk/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/SeqMonk/slack-desc b/academic/SeqMonk/slack-desc new file mode 100644 index 0000000000..632f4c5de1 --- /dev/null +++ b/academic/SeqMonk/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 ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +SeqMonk: SeqMonk (A Mapped Sequence Analysis tool) +SeqMonk: +SeqMonk: SeqMonk is a tool for viewing and analysing mapped sequence data. +SeqMonk: It was initially written to cope with remapping experiment data +SeqMonk: from next generation sequencers, but could be applied to any +SeqMonk: dataset consisting of a series of mapped genomic regions. The +SeqMonk: program allows you to visualise the positions of your mapped +SeqMonk: regions against an annotated genome and to quantify the data in +SeqMonk: order to make comparisons between data sets. +SeqMonk: +SeqMonk: https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/ |