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>

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/