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| -rw-r--r-- | academic/tophat/README | 10 | ||||
| -rw-r--r-- | academic/tophat/References | 13 | ||||
| -rw-r--r-- | academic/tophat/slack-desc | 19 | ||||
| -rw-r--r-- | academic/tophat/tophat.SlackBuild | 100 | ||||
| -rw-r--r-- | academic/tophat/tophat.info | 10 |
5 files changed, 152 insertions, 0 deletions
diff --git a/academic/tophat/README b/academic/tophat/README new file mode 100644 index 0000000000000..79c93851ff938 --- /dev/null +++ b/academic/tophat/README @@ -0,0 +1,10 @@ +TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns +RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput +short read aligner Bowtie, and then analyzes the mapping results to +identify splice junctions between exons. + +TopHat is a collaborative effort between the Institute of Genetic +Medicine at Johns Hopkins University, the Departments of Mathematics +and Molecular and Cell Biology at the University of California, +Berkeley and the Department of Stem Cell and Regenerative Biology at +Harvard University. diff --git a/academic/tophat/References b/academic/tophat/References new file mode 100644 index 0000000000000..0e7deda7d172f --- /dev/null +++ b/academic/tophat/References @@ -0,0 +1,13 @@ +Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice +junctions with RNA-Seq. Bioinformatics doi:10.1093/bioinformatics/btp120 + +Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory- +efficient alignment of short DNA sequences to the human genome. Genome +Biology 10:R25. + +Kim D and Salzberg SL. TopHat-Fusion: an algorithm for discovery of +novel fusion transcripts. Genome Biology 2011, 12:R72 + +Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. +TopHat2: accurate alignment of transcriptomes in the presence of +insertions, deletions and gene fusions. . Genome Biology 2011, 14:R36 diff --git a/academic/tophat/slack-desc b/academic/tophat/slack-desc new file mode 100644 index 0000000000000..77d54ce3ac524 --- /dev/null +++ b/academic/tophat/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------------------------------------------------------| +tophat: tophat (Splice junction mapper for RNA-Seq reads) +tophat: +tophat: TopHat is a fast splice junction mapper for RNA-Seq reads. It +tophat: aligns RNA-Seq reads to mammalian-sized genomes using the ultra +tophat: high-throughput short read aligner Bowtie, and then analyzes the +tophat: mapping results to identify splice junctions between exons. +tophat: +tophat: Home: http://tophat.cbcb.umd.edu/ +tophat: Reference: /usr/doc/tophat-2.0.10/References +tophat: +tophat: diff --git a/academic/tophat/tophat.SlackBuild b/academic/tophat/tophat.SlackBuild new file mode 100644 index 0000000000000..fa0a20b54ff27 --- /dev/null +++ b/academic/tophat/tophat.SlackBuild @@ -0,0 +1,100 @@ +#!/bin/sh + +# Slackware build script for tophat + +# Copyright 2013 Petar Petrov, petar.petrov@student.oulu.fi +# 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=tophat +VERSION=${VERSION:-2.0.10} +BUILD=${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 +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 {} \; + +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +./configure \ + --prefix=/usr \ + --libdir=/usr/lib${LIBDIRSUFFIX} \ + --sysconfdir=/etc \ + --with-boost-libdir=/usr/lib${LIBDIRSUFFIX} \ + --localstatedir=/var \ + --mandir=/usr/man \ + --build=$ARCH-slackware-linux + +make +make install DESTDIR=$PKG + +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 \ + AUTHORS COPYING INSTALL LICENSE NEWS README THANKS \ + $PKG/usr/doc/$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 +cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} diff --git a/academic/tophat/tophat.info b/academic/tophat/tophat.info new file mode 100644 index 0000000000000..7b2b55da95e7c --- /dev/null +++ b/academic/tophat/tophat.info @@ -0,0 +1,10 @@ +PRGNAM="tophat" +VERSION="2.0.10" +HOMEPAGE="http://tophat.cbcb.umd.edu/" +DOWNLOAD="http://tophat.cbcb.umd.edu/downloads/tophat-2.0.10.tar.gz" +MD5SUM="dd99465d44f9e5255d6480b8d5ab80ca" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="bowtie2 samtools" +MAINTAINER="Petar Petrov" +EMAIL="petar.petrov@student.oulu.fi" |