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| -rw-r--r-- | academic/cistrome-conductGO/README | 24 | ||||
| -rw-r--r-- | academic/cistrome-conductGO/bioconductor.txt | 3 | ||||
| -rw-r--r-- | academic/cistrome-conductGO/cistrome-conductGO.SlackBuild | 77 | ||||
| -rw-r--r-- | academic/cistrome-conductGO/cistrome-conductGO.info | 10 | ||||
| -rw-r--r-- | academic/cistrome-conductGO/slack-desc | 19 |
5 files changed, 133 insertions, 0 deletions
diff --git a/academic/cistrome-conductGO/README b/academic/cistrome-conductGO/README new file mode 100644 index 0000000000000..a0ff4fb3b51f6 --- /dev/null +++ b/academic/cistrome-conductGO/README @@ -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. diff --git a/academic/cistrome-conductGO/bioconductor.txt b/academic/cistrome-conductGO/bioconductor.txt new file mode 100644 index 0000000000000..415c9f2db0a50 --- /dev/null +++ b/academic/cistrome-conductGO/bioconductor.txt @@ -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")) diff --git a/academic/cistrome-conductGO/cistrome-conductGO.SlackBuild b/academic/cistrome-conductGO/cistrome-conductGO.SlackBuild new file mode 100644 index 0000000000000..7f7ca6f2a5cfe --- /dev/null +++ b/academic/cistrome-conductGO/cistrome-conductGO.SlackBuild @@ -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} diff --git a/academic/cistrome-conductGO/cistrome-conductGO.info b/academic/cistrome-conductGO/cistrome-conductGO.info new file mode 100644 index 0000000000000..a5edc11c01fe8 --- /dev/null +++ b/academic/cistrome-conductGO/cistrome-conductGO.info @@ -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" diff --git a/academic/cistrome-conductGO/slack-desc b/academic/cistrome-conductGO/slack-desc new file mode 100644 index 0000000000000..04ffa71c742fb --- /dev/null +++ b/academic/cistrome-conductGO/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-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: |