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academic/cufflinks: Added (reference-guided assembler for RNA-Seq).
Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>
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17
academic/cufflinks/README
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academic/cufflinks/README
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Cufflinks assembles transcripts, estimates their abundances, and tests
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for differential expression and regulation in RNA-Seq samples. It
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accepts aligned RNA-Seq reads and assembles the alignments into a
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parsimonious set of transcripts. Cufflinks then estimates the relative
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abundances of these transcripts based on how many reads support each
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one, taking into account biases in library preparation protocols.
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Cufflinks is a collaborative effort between the Laboratory for
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Mathematical and Computational Biology, led by Lior Pachter at UC
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Berkeley, Steven Salzberg's computational genomics group at the
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Institute of Genetic Medicine at Johns Hopkins University, and Barbara
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Wold's lab at Caltech.
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Reference:
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Ali Mortazavi, Brian A Williams, Kenneth McCue, Lorian Schaeffer and
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Barbara Wold, "Mapping and quantifying mammalian transcriptomes by
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RNA-Seq", Nature Methods, volume 5, 621 - 628 (2008)
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37
academic/cufflinks/References
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academic/cufflinks/References
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Publications
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Trapnell C, Williams BA, Pertea G, Mortazavi AM, Kwan G, van Baren MJ,
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Salzberg SL, Wold B, Pachter L. Transcript assembly and quantification
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by RNA-Seq reveals unannotated transcripts and isoform switching
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during cell differentiation
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Nature Biotechnology doi:10.1038/nbt.1621
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Roberts A, Trapnell C, Donaghey J, Rinn JL, Pachter L. Improving RNA-
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Seq expression estimates by correcting for fragment bias
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Genome Biology doi:10.1186/gb-2011-12-3-r22
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Roberts A, Pimentel H, Trapnell C, Pachter L. Identification of novel
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transcripts in annotated genomes using RNA-Seq
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Bioinformatics doi:10.1093/bioinformatics/btr355
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Trapnell C, Hendrickson D,Sauvageau S, Goff L, Rinn JL, Pachter L
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Differential analysis of gene regulation at transcript resolution with
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RNA-seq
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Nature Biotechnology doi:10.1038/nbt.2450
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REFERENCES
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---------------------------
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Cufflinks builds on many ideas, including some
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proposed in the following papers:
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Ali Mortazavi, Brian A Williams, Kenneth McCue, Lorian Schaeffer and Barbara
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Wold, "Mapping and quantifying mammalian transcriptomes by RNA-Seq",Nature
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Methods, volume 5, 621 - 628 (2008)
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Hui Jiang and Wing Hung Wong, "Statistical Inferences for isoform expression",
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Bioinformatics, 2009 25(8):1026-1032
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Nicholas Eriksson, Lior Pachter, Yumi Mitsuya, Soo-Yon Rhee, Chunlin Wang,
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Baback Gharizadeh, Mostafa Ronaghi, Robert W. Shafer, Niko Beerenwinkel, "Viral
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population estimation using pyrosequencing", PLoS Computational Biology,
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4(5):e1000074
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107
academic/cufflinks/cufflinks.SlackBuild
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academic/cufflinks/cufflinks.SlackBuild
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#!/bin/sh
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# Slackware build script for cufflinks
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# Copyright 2013 Petar Petrov, petar.petrov@student.oulu.fi
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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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# With help from Archlinux AUR and Gentoo:
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# https://aur.archlinux.org/packages/cufflinks/
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# http://euscan.iksaif.net/package/sci-biology/cufflinks/
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PRGNAM=cufflinks
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VERSION=${VERSION:-2.1.1}
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BUILD=${BUILD:-1}
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TAG=${TAG:-_SBo}
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if [ -z "$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 $PRGNAM-$VERSION
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tar xvf $CWD/$PRGNAM-$VERSION.tar.gz
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cd $PRGNAM-$VERSION
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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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export EIGEN_CPPFLAGS="-I/usr/include/eigen3"
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CFLAGS="$SLKCFLAGS" \
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CXXFLAGS="$SLKCFLAGS" \
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./configure \
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--prefix=/usr \
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--libdir=/usr/lib${LIBDIRSUFFIX} \
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--sysconfdir=/etc \
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--disable-optim \
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--with-boost-libdir=/usr/lib${LIBDIRSUFFIX} \
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--localstatedir=/var \
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--mandir=/usr/man \
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--build=$ARCH-slackware-linux
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make
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make install DESTDIR=$PKG
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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-$VERSION
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cp -a \
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AUTHORS LICENSE README \
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$PKG/usr/doc/$PRGNAM-$VERSION
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cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
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cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References
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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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10
academic/cufflinks/cufflinks.info
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academic/cufflinks/cufflinks.info
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PRGNAM="cufflinks"
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VERSION="2.1.1"
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HOMEPAGE="http://cufflinks.cbcb.umd.edu/"
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DOWNLOAD="http://cufflinks.cbcb.umd.edu/downloads/cufflinks-2.1.1.tar.gz"
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MD5SUM="3c1f34264122565b1697706a5f0fd242"
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DOWNLOAD_x86_64=""
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MD5SUM_x86_64=""
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REQUIRES="eigen3 samtools"
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MAINTAINER="Petar Petrov"
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EMAIL="petar.petrov@student.oulu.fi"
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19
academic/cufflinks/slack-desc
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19
academic/cufflinks/slack-desc
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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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cufflinks: cufflinks (A reference-guided assembler for RNA-Seq experiments)
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cufflinks:
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cufflinks: Cufflinks assembles transcripts, estimates their abundances,
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cufflinks: and tests for differential expression and regulation in RNA-
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cufflinks: Seq samples. It accepts aligned RNA-Seq reads and assembles
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cufflinks: the alignments into a parsimonious set of transcripts.
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cufflinks:
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cufflinks: Home: http://cufflinks.cbcb.umd.edu/
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cufflinks: References: /usr/doc/cufflinks-2.1.1/References
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cufflinks:
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cufflinks:
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