academic/cistrome-extra: Added (Cistrome extra apps)
Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>
This commit is contained in:
Petar Petrov
Willy Sudiarto Raharjo
parent
2e35245d33
commit
55129a3e91
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The cistrome refers to "the set of cis-acting targets of a trans-
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acting factor on a genome-wide scale, also known as the in vivo
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genome-wide location of transcription factor binding-sites or histone
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modifications". The term cistrome is a portmanteau of cistron + genome
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and was coined by investigators at the Dana-Farber Cancer Institute
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and Harvard Medical School.
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This is cistrome-extra apps, part of the Cistrome-Applications-Harvard
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project.
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#!/bin/sh
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# Slackware build script for cistrome-extra
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# Copyright 2016 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=cistrome-extra
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VERSION=${VERSION:-git_20150729_7bcbf79}
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BUILD=${BUILD:-1}
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TAG=${TAG:-_SBo}
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SRCNAM=cistrome-cistrome-applications-harvard
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SRCVER=7bcbf7953a8b
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if [ -z "$ARCH" ]; then
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case "$( uname -m )" in
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i?86) ARCH=i486 ;;
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arm*) ARCH=arm ;;
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*) ARCH=$( 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" = "i486" ]; then
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SLKCFLAGS="-O2 -march=i486 -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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rm -rf $PKG
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mkdir -p $TMP $PKG $OUTPUT
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cd $TMP
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rm -rf $SRCNAM-$SRCVER
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if [ -e $CWD/$SRCVER.zip ]; then
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unzip $CWD/$SRCVER.zip
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else
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unzip $CWD/$SRCNAM-$SRCVER.zip
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fi
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cd $SRCNAM-$SRCVER
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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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cd cistrome-extra-apps
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python setup.py build
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python setup.py install --root=$PKG
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cd ..
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find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \
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| cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true
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mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
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cp -a LICENSE.txt $PKG/usr/doc/$PRGNAM-$VERSION
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cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
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# Ugene expects this to be called like that
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cd $PKG/usr/bin
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ln -s PCGA.py peak2gene.py
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mkdir -p $PKG/install
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cat $CWD/slack-desc > $PKG/install/slack-desc
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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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PRGNAM="cistrome-extra"
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VERSION="git_20150729_7bcbf79"
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HOMEPAGE="http://cistrome.org/"
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DOWNLOAD="https://bitbucket.org/cistrome/cistrome-applications-harvard/get/7bcbf7953a8b.zip"
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MD5SUM="39e85034e56b82eb445bb2a9744c438e"
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DOWNLOAD_x86_64=""
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MD5SUM_x86_64=""
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REQUIRES=""
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MAINTAINER="Petar Petrov"
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EMAIL="slackalaxy@gmail.com"
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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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cistrome-extra: cistrome-extra (Cistrome Applications Harvard extra apps)
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cistrome-extra:
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cistrome-extra: This is cistrome-extra, part of the Cistrome-Applications-Harvard
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cistrome-extra: project.
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cistrome-extra:
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cistrome-extra:
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cistrome-extra:
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cistrome-extra:
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cistrome-extra:
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cistrome-extra:
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cistrome-extra:
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