mirror of
https://github.com/SlackBuildsOrg/slackbuilds
synced 2024-09-28 15:21:00 +02:00
academic/cistrome-conductGO: Added (find the highest expressed TFs)
This commit is contained in:
parent
aad6293dd9
commit
2e35245d33
5 changed files with 133 additions and 0 deletions
24
academic/cistrome-conductGO/README
Normal file
24
academic/cistrome-conductGO/README
Normal file
|
@ -0,0 +1,24 @@
|
|||
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-conductGO (GO analysis): a galaxy tool to find the
|
||||
top-n highest expressed TFs. For a list of input genes, this tool uses
|
||||
R/BioC packages (GO, GOstats) to identify over represented GO terms.
|
||||
|
||||
GO analysis depends on several R script tools (GOstats, GO.db,
|
||||
hgu133a.db, hgu133b.db, hgu133plus2.db, hgu95av2.db, mouse430a2.db,
|
||||
celegans.db, drosophila2.db, org.Hs.eg.db, org.Mm.eg.db, org.Ce.eg.db,
|
||||
org.Dm.eg.db). Visit https://bioconductor.org/ for details and see
|
||||
"biocondictor.txt" (also copied to the documentation folder of the
|
||||
created package) for batch installation of the required Bioconductor
|
||||
Packages.
|
||||
|
||||
NOTE!
|
||||
This just repackages the script redistributed by the UniPro Ugene
|
||||
project, part of their External Tools package. This is the reason the
|
||||
homepage link points to Ugene. The source is hosted on Source Forge by
|
||||
the SlackBuild maintainer.
|
3
academic/cistrome-conductGO/bioconductor.txt
Normal file
3
academic/cistrome-conductGO/bioconductor.txt
Normal file
|
@ -0,0 +1,3 @@
|
|||
## try http:// if https:// URLs are not supported
|
||||
source("https://bioconductor.org/biocLite.R")
|
||||
biocLite(c("GOstats", "GO.db", "hgu133a.db", "hgu133b.db", "hgu133plus2.db", "hgu95av2.db", "mouse430a2.db", "celegans.db", "drosophila2.db", "org.Hs.eg.db", "org.Mm.eg.db", "org.Ce.eg.db", "org.Dm.eg.db"))
|
77
academic/cistrome-conductGO/cistrome-conductGO.SlackBuild
Normal file
77
academic/cistrome-conductGO/cistrome-conductGO.SlackBuild
Normal file
|
@ -0,0 +1,77 @@
|
|||
#!/bin/sh
|
||||
|
||||
# Slackware build script for cistrome-conductGO
|
||||
|
||||
# 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-conductGO
|
||||
VERSION=${VERSION:-1.0}
|
||||
BUILD=${BUILD:-1}
|
||||
TAG=${TAG:-_SBo}
|
||||
|
||||
if [ -z "$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 $PRGNAM-$VERSION
|
||||
tar xvf $CWD/$PRGNAM-$VERSION.tar.gz
|
||||
cd $PRGNAM-$VERSION
|
||||
|
||||
install -D -m755 go_analysis.py $PKG/usr/bin/go_analysis.py
|
||||
install -D -m644 utils.R $PKG/usr/share/$PRGNAM/utils.R
|
||||
|
||||
mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
|
||||
cp -a $CWD/bioconductor.txt $PKG/usr/doc/$PRGNAM-$VERSION
|
||||
cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
|
||||
|
||||
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}
|
10
academic/cistrome-conductGO/cistrome-conductGO.info
Normal file
10
academic/cistrome-conductGO/cistrome-conductGO.info
Normal file
|
@ -0,0 +1,10 @@
|
|||
PRGNAM="cistrome-conductGO"
|
||||
VERSION="1.0"
|
||||
HOMEPAGE="http://ugene.net/external.html"
|
||||
DOWNLOAD="http://sourceforge.net/projects/sboppetrov/files/ugene/cistrome-conductGO/cistrome-conductGO-1.0.tar.gz"
|
||||
MD5SUM="f15648c693460b07f285008b6c061858"
|
||||
DOWNLOAD_x86_64=""
|
||||
MD5SUM_x86_64=""
|
||||
REQUIRES="R"
|
||||
MAINTAINER="Petar Petrov"
|
||||
EMAIL="slackalaxy@gmail.com"
|
19
academic/cistrome-conductGO/slack-desc
Normal file
19
academic/cistrome-conductGO/slack-desc
Normal file
|
@ -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-conductGO: cistrome-conductGO (find the top-n highest expressed TFs)
|
||||
cistrome-conductGO:
|
||||
cistrome-conductGO: A galaxy tool to find the top-n highest expressed TFs.
|
||||
cistrome-conductGO:
|
||||
cistrome-conductGO:
|
||||
cistrome-conductGO:
|
||||
cistrome-conductGO:
|
||||
cistrome-conductGO:
|
||||
cistrome-conductGO:
|
||||
cistrome-conductGO:
|
||||
cistrome-conductGO:
|
Loading…
Reference in a new issue