From 55129a3e91331cb57800584ad07bd3c93fa13f89 Mon Sep 17 00:00:00 2001 From: Petar Petrov Date: Sun, 5 Jun 2016 15:35:47 +0300 Subject: [PATCH] academic/cistrome-extra: Added (Cistrome extra apps) Signed-off-by: Willy Sudiarto Raharjo --- academic/cistrome-extra/README | 9 ++ .../cistrome-extra/cistrome-extra.SlackBuild | 101 ++++++++++++++++++ academic/cistrome-extra/cistrome-extra.info | 10 ++ academic/cistrome-extra/slack-desc | 19 ++++ 4 files changed, 139 insertions(+) create mode 100644 academic/cistrome-extra/README create mode 100644 academic/cistrome-extra/cistrome-extra.SlackBuild create mode 100644 academic/cistrome-extra/cistrome-extra.info create mode 100644 academic/cistrome-extra/slack-desc diff --git a/academic/cistrome-extra/README b/academic/cistrome-extra/README new file mode 100644 index 0000000000..0dd4a06ea4 --- /dev/null +++ b/academic/cistrome-extra/README @@ -0,0 +1,9 @@ +The cistrome refers to "the set of cis-acting targets of a trans- +acting factor on a genome-wide scale, also known as the in vivo +genome-wide location of transcription factor binding-sites or histone +modifications". The term cistrome is a portmanteau of cistron + genome +and was coined by investigators at the Dana-Farber Cancer Institute +and Harvard Medical School. + +This is cistrome-extra apps, part of the Cistrome-Applications-Harvard +project. diff --git a/academic/cistrome-extra/cistrome-extra.SlackBuild b/academic/cistrome-extra/cistrome-extra.SlackBuild new file mode 100644 index 0000000000..9ed2e2046f --- /dev/null +++ b/academic/cistrome-extra/cistrome-extra.SlackBuild @@ -0,0 +1,101 @@ +#!/bin/sh + +# Slackware build script for cistrome-extra + +# Copyright 2016 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=cistrome-extra +VERSION=${VERSION:-git_20150729_7bcbf79} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +SRCNAM=cistrome-cistrome-applications-harvard +SRCVER=7bcbf7953a8b + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i486 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +CWD=$(pwd) +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i486" ]; then + SLKCFLAGS="-O2 -march=i486 -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 + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $SRCNAM-$SRCVER + +if [ -e $CWD/$SRCVER.zip ]; then + unzip $CWD/$SRCVER.zip +else + unzip $CWD/$SRCNAM-$SRCVER.zip +fi + +cd $SRCNAM-$SRCVER +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 {} \; + +cd cistrome-extra-apps +python setup.py build +python setup.py install --root=$PKG +cd .. + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a LICENSE.txt $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +# Ugene expects this to be called like that +cd $PKG/usr/bin +ln -s PCGA.py peak2gene.py + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} diff --git a/academic/cistrome-extra/cistrome-extra.info b/academic/cistrome-extra/cistrome-extra.info new file mode 100644 index 0000000000..8c5e783971 --- /dev/null +++ b/academic/cistrome-extra/cistrome-extra.info @@ -0,0 +1,10 @@ +PRGNAM="cistrome-extra" +VERSION="git_20150729_7bcbf79" +HOMEPAGE="http://cistrome.org/" +DOWNLOAD="https://bitbucket.org/cistrome/cistrome-applications-harvard/get/7bcbf7953a8b.zip" +MD5SUM="39e85034e56b82eb445bb2a9744c438e" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/cistrome-extra/slack-desc b/academic/cistrome-extra/slack-desc new file mode 100644 index 0000000000..b67a22461d --- /dev/null +++ b/academic/cistrome-extra/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------------------------------------------------------| +cistrome-extra: cistrome-extra (Cistrome Applications Harvard extra apps) +cistrome-extra: +cistrome-extra: This is cistrome-extra, part of the Cistrome-Applications-Harvard +cistrome-extra: project. +cistrome-extra: +cistrome-extra: +cistrome-extra: +cistrome-extra: +cistrome-extra: +cistrome-extra: +cistrome-extra: