diff options
author | Petar Petrov <slackalaxy@gmail.com> | 2018-12-24 11:15:14 +0700 |
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committer | Willy Sudiarto Raharjo <willysr@slackbuilds.org> | 2018-12-24 22:16:51 +0700 |
commit | 2183ac8328445578506cf475014eb1bf51353504 (patch) | |
tree | 997d5242f98fb2fe8446f86b6093939338aa7729 | |
parent | 201f40382197fbf0baf90fbafd016efb5567a7f8 (diff) |
academic/stringtie: Added (Assembler of RNA-Seq alignments).
Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>
-rw-r--r-- | academic/stringtie/README | 11 | ||||
-rw-r--r-- | academic/stringtie/slack-desc | 19 | ||||
-rw-r--r-- | academic/stringtie/stringtie.SlackBuild | 91 | ||||
-rw-r--r-- | academic/stringtie/stringtie.info | 10 |
4 files changed, 131 insertions, 0 deletions
diff --git a/academic/stringtie/README b/academic/stringtie/README new file mode 100644 index 0000000000000..0ffb8ddea5edc --- /dev/null +++ b/academic/stringtie/README @@ -0,0 +1,11 @@ +StringTie is a fast and highly efficient assembler of RNA-Seq +alignments into potential transcripts. It uses a novel network flow +algorithm as well as an optional de novo assembly step to assemble and +quantitate full-length transcripts representing multiple splice +variants for each gene locus. Its input can include not only the +alignments of raw reads used by other transcript assemblers, but also +alignments longer sequences that have been assembled from those reads. + +In order to identify differentially expressed genes between +experiments, StringTie's output can be processed by specialized +software like Ballgown, Cuffdiff or other programs (DESeq2, edgeR). diff --git a/academic/stringtie/slack-desc b/academic/stringtie/slack-desc new file mode 100644 index 0000000000000..8f72782c51c9c --- /dev/null +++ b/academic/stringtie/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------------------------------------------------------| +stringtie: stringtie (Assembler of RNA-Seq alignments) +stringtie: +stringtie: StringTie is a fast and highly efficient assembler of RNA-Seq +stringtie: alignments into potential transcripts. It uses a novel network +stringtie: flow algorithm as well as an optional de novo assembly step to +stringtie: assemble and quantitate full-length transcripts representing +stringtie: multiple splice variants for each gene locus. +stringtie: +stringtie: Home: http://ccb.jhu.edu/software/stringtie/ +stringtie: +stringtie: diff --git a/academic/stringtie/stringtie.SlackBuild b/academic/stringtie/stringtie.SlackBuild new file mode 100644 index 0000000000000..51f471e71a4e3 --- /dev/null +++ b/academic/stringtie/stringtie.SlackBuild @@ -0,0 +1,91 @@ +#!/bin/sh + +# Slackware build script for stringtie + +# Copyright 2018 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=stringtie +VERSION=${VERSION:-1.3.5} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +CWD=$(pwd) +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -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 {} \; + +CXXFLAGS="$SLKCFLAGS" \ +make release + +install -D -m755 $PRGNAM $PKG/usr/bin/$PRGNAM + +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 README.md \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +# Copy the slack-desc (and a custom doinst.sh if necessary) into ./install +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/stringtie/stringtie.info b/academic/stringtie/stringtie.info new file mode 100644 index 0000000000000..6ab44c841aa6f --- /dev/null +++ b/academic/stringtie/stringtie.info @@ -0,0 +1,10 @@ +PRGNAM="stringtie" +VERSION="1.3.5" +HOMEPAGE="http://ccb.jhu.edu/software/stringtie/" +DOWNLOAD="https://github.com/gpertea/stringtie/archive/v1.3.5/stringtie-1.3.5.tar.gz" +MD5SUM="64e5a271dd1b4408728c5f16ce1222ff" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" |