From 0a2f999f14efb22ee44fcaf3da61cd5a1831a9d5 Mon Sep 17 00:00:00 2001 From: Rob van Nues Date: Tue, 15 May 2018 08:40:06 +0100 Subject: academic/STAR: Added (Spliced Transcripts Alignment to a Reference). Signed-off-by: David Spencer --- academic/STAR/README | 7 +++ academic/STAR/STAR.SlackBuild | 96 ++++++++++++++++++++++++++++++++++++++++ academic/STAR/STAR.info | 10 +++++ academic/STAR/reproducible.patch | 14 ++++++ academic/STAR/slack-desc | 19 ++++++++ 5 files changed, 146 insertions(+) create mode 100644 academic/STAR/README create mode 100644 academic/STAR/STAR.SlackBuild create mode 100644 academic/STAR/STAR.info create mode 100644 academic/STAR/reproducible.patch create mode 100644 academic/STAR/slack-desc (limited to 'academic/STAR') diff --git a/academic/STAR/README b/academic/STAR/README new file mode 100644 index 0000000000..3608afef93 --- /dev/null +++ b/academic/STAR/README @@ -0,0 +1,7 @@ +STAR aligns short and long RNA-seq reads to a reference genome using +uncompressed suffix arrays, resulting in fast, accurate mapping. +STAR is capable of unbiased de novo detection of canonical junctions, +can discover non-canonical splices and chimeric (fusion) transcripts and +can map full-length RNA sequences. + +Reference: https://www.ncbi.nlm.nih.gov/pubmed/23104886 diff --git a/academic/STAR/STAR.SlackBuild b/academic/STAR/STAR.SlackBuild new file mode 100644 index 0000000000..aa89b2927f --- /dev/null +++ b/academic/STAR/STAR.SlackBuild @@ -0,0 +1,96 @@ +#!/bin/sh + +# Slackware build script for STAR + +# Copyright 2018 Rob van Nues +# 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=STAR +VERSION=${VERSION:-2.6.0c} +BUILD=${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" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC -fsigned-char" + LIBDIRSUFFIX="64" +else + echo "Sorry, this program does not run/compile on your architecture ($ARCH)" + exit 1 +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 {} \; + +# https://sources.debian.org/data/main/r/rna-star/2.6.0b+dfsg-1/debian/patches/reproducible.patch +# (with minor modification) +patch -p1 < $CWD/reproducible.patch + +cd source + + make ${PRGNAM} CFLAGS="$SLKCFLAGS" CXXFLAGSextra="$SLKCFLAGS" + + mkdir -p $PKG/usr/bin + install -Dm755 $PRGNAM "$PKG/usr/bin/${PRGNAM}" + + make clean + make ${PRGNAM}long CXXFLAGSextra="$CXXFLAGS" + install -Dm755 ${PRGNAM}long "$PKG/usr/bin/${PRGNAM}long" + +cd .. + +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-$VERSION +cp -a \ + source/parametersDefault doc/${PRGNAM}manual.pdf CHANGES.md LICENSE README.md RELEASEnotes.md \ + $PKG/usr/doc/$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/STAR/STAR.info b/academic/STAR/STAR.info new file mode 100644 index 0000000000..2ba024dafd --- /dev/null +++ b/academic/STAR/STAR.info @@ -0,0 +1,10 @@ +PRGNAM="STAR" +VERSION="2.6.0c" +HOMEPAGE="https://github.com/alexdobin/STAR" +DOWNLOAD="UNSUPPORTED" +MD5SUM="" +DOWNLOAD_x86_64="https://github.com/alexdobin/STAR/archive/2.6.0c/STAR-2.6.0c.tar.gz" +MD5SUM_x86_64="014e44faa78c13e781bb74d9b5cf00d8" +REQUIRES="" +MAINTAINER="Rob van Nues" +EMAIL="rvnues { at } disroot { dot } org" diff --git a/academic/STAR/reproducible.patch b/academic/STAR/reproducible.patch new file mode 100644 index 0000000000..f340376023 --- /dev/null +++ b/academic/STAR/reproducible.patch @@ -0,0 +1,14 @@ +Description: make build reproducible + Stops build hostname and directory from being recorded in the artifact. +Author: Sascha Steinbiss +--- a/source/Makefile ++++ b/source/Makefile +@@ -18,7 +18,7 @@ + LDFLAGS_Mac_static :=-pthread -lz -static-libgcc htslib/libhts.a + LDFLAGS_gdb += $(LDFLAGS_shared) + +-COMPTIMEPLACE := -D'COMPILATION_TIME_PLACE="$(shell echo `date` $(HOSTNAME):`pwd`)"' ++COMPTIMEPLACE := -D'COMPILATION_TIME_PLACE=""' + + CXXFLAGS_common := -pipe -std=c++11 -Wall -Wextra -fopenmp $(COMPTIMEPLACE) $(CCFLAGS_common_add) + CXXFLAGS_main += -O3 $(CXXFLAGS_common) diff --git a/academic/STAR/slack-desc b/academic/STAR/slack-desc new file mode 100644 index 0000000000..433a7dfbb0 --- /dev/null +++ b/academic/STAR/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------------------------------------------------------| +STAR: STAR (Spliced Transcripts Alignment to a Reference) +STAR: +STAR: STAR aligns short and long RNA-seq reads to a reference genome using +STAR: uncompressed suffix arrays, resulting in fast, accurate mapping. +STAR: STAR is capable of unbiased de novo detection of canonical junctions, +STAR: can discover non-canonical splices and chimeric (fusion) transcripts +STAR: and can map full-length RNA sequences. +STAR: +STAR: https://github.com/alexdobin/STAR +STAR: Reference: https://www.ncbi.nlm.nih.gov/pubmed/23104886 +STAR: -- cgit v1.2.3-65-gdbad