diff options
Diffstat (limited to 'academic/ucsc-blat')
| -rw-r--r-- | academic/ucsc-blat/LICENSE | 8 | ||||
| -rw-r--r-- | academic/ucsc-blat/README | 11 | ||||
| -rw-r--r-- | academic/ucsc-blat/References | 2 | ||||
| -rw-r--r-- | academic/ucsc-blat/slack-desc | 19 | ||||
| -rw-r--r-- | academic/ucsc-blat/ucsc-blat.SlackBuild | 93 | ||||
| -rw-r--r-- | academic/ucsc-blat/ucsc-blat.info | 10 |
6 files changed, 143 insertions, 0 deletions
diff --git a/academic/ucsc-blat/LICENSE b/academic/ucsc-blat/LICENSE new file mode 100644 index 0000000000000..d2d7cd5a27ce4 --- /dev/null +++ b/academic/ucsc-blat/LICENSE @@ -0,0 +1,8 @@ +BLAT was written by Jim Kent. Sources and executables to run +batch jobs on your own server are available free for academic, +personal, and non-profit purposes. Non-exclusive commercial licenses +are also available. + +For information about commercial licensing of Blat, see the Kent +Informatics website (http://www.kentinformatics.com/) or contact +kent@soe.ucsc.edu. diff --git a/academic/ucsc-blat/README b/academic/ucsc-blat/README new file mode 100644 index 0000000000000..8f47ce6e07695 --- /dev/null +++ b/academic/ucsc-blat/README @@ -0,0 +1,11 @@ +BLAT is a bioinformatics software tool which performs rapid mRNA/DNA +and cross-species protein alignments. BLAT is more accurate and 500 +times faster than popular existing tools for mRNA/DNA alignments and +50 times faster for protein alignments at sensitivity settings +typically used when comparing vertebrate sequences. + +For details and citation: +Source: Kent, W.J. 2002. BLAT -- The BLAST-Like Alignment Tool. +Genome Research 4: 656-664. + +This just repackages the binaries provided from upstream. diff --git a/academic/ucsc-blat/References b/academic/ucsc-blat/References new file mode 100644 index 0000000000000..f8c9739955901 --- /dev/null +++ b/academic/ucsc-blat/References @@ -0,0 +1,2 @@ +Source: Kent, W.J. 2002. BLAT -- The BLAST-Like Alignment Tool. +Genome Research 4: 656-664. diff --git a/academic/ucsc-blat/slack-desc b/academic/ucsc-blat/slack-desc new file mode 100644 index 0000000000000..cb6eff3cf2a60 --- /dev/null +++ b/academic/ucsc-blat/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------------------------------------------------------| +ucsc-blat: ucsc-blat (BLAT -- The BLAST-Like Alignment Tool) +ucsc-blat: +ucsc-blat: BLAT is a bioinformatics software a tool which performs rapid +ucsc-blat: mRNA/DNA and cross-species protein alignments. BLAT is more accurate +ucsc-blat: and 500 times faster than popular existing tools for mRNA/DNA +ucsc-blat: alignments and 50 times faster for protein alignments at sensitivity +ucsc-blat: settings typically used when comparing vertebrate sequences. +ucsc-blat: +ucsc-blat: Home: http://www.kentinformatics.com/ +ucsc-blat: References:/usr/doc/ucsc-blat-$VERSION/References +ucsc-blat: diff --git a/academic/ucsc-blat/ucsc-blat.SlackBuild b/academic/ucsc-blat/ucsc-blat.SlackBuild new file mode 100644 index 0000000000000..e207ea3e0dd81 --- /dev/null +++ b/academic/ucsc-blat/ucsc-blat.SlackBuild @@ -0,0 +1,93 @@ +#!/bin/sh + +# Slackware build script for ucsc-blat + +# Copyright 2013 Petar Petrov, ppetrov@paju.oulu.fi +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +PRGNAM=ucsc-blat +VERSION=${VERSION:-34} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +SRCNAM=blatSuite + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i386 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +CWD=$(pwd) +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +set -e + +if [ "$ARCH" != "i386" ] && [ "$ARCH" != "x86_64" ]; then + printf "\n\n$ARCH is not supported... \n" + exit 1 +fi + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$PRGVER +mkdir $PRGNAM-$PRGVER +cd $PRGNAM-$PRGVER +unzip $CWD/${SRCNAM}.${VERSION}.zip +chown -R root:root . +find . \ + \( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \ + -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ + -exec chmod 644 {} \; + +# Install the precompiled binaries. +install -D -m755 blat $PKG/usr/bin/blat +install -D -m755 faToNib $PKG/usr/bin/faToNib +install -D -m755 faToTwoBit $PKG/usr/bin/faToTwoBit +install -D -m755 gfClient $PKG/usr/bin/gfClient +install -D -m755 gfServer $PKG/usr/bin/gfServer +install -D -m755 nibFrag $PKG/usr/bin/nibFrag +install -D -m755 pslPretty $PKG/usr/bin/pslPretty +install -D -m755 pslReps $PKG/usr/bin/pslReps +install -D -m755 pslSort $PKG/usr/bin/pslSort +install -D -m755 twoBitInfo $PKG/usr/bin/twoBitInfo +install -D -m755 twoBitToFa $PKG/usr/bin/twoBitToFa +install -D -m755 webBlat $PKG/usr/bin/webBlat + +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 version.doc $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References +cat $CWD/LICENSE > $PKG/usr/doc/$PRGNAM-$VERSION/LICENSE + +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/ucsc-blat/ucsc-blat.info b/academic/ucsc-blat/ucsc-blat.info new file mode 100644 index 0000000000000..da78e80fff291 --- /dev/null +++ b/academic/ucsc-blat/ucsc-blat.info @@ -0,0 +1,10 @@ +PRGNAM="ucsc-blat" +VERSION="34" +HOMEPAGE="http://users.soe.ucsc.edu/~kent/" +DOWNLOAD="http://hgwdev.cse.ucsc.edu/~kent/exe/linux/blatSuite.34.zip" +MD5SUM="ec9fbe02fed2f15051893001da5db767" +DOWNLOAD_x86_64="http://hgwdev.cse.ucsc.edu/~kent/exe/opteron/blatSuite.34.zip" +MD5SUM_x86_64="bf9042aa85a04ce85b24cef11011faee" +REQUIRES="" +MAINTAINER="Petar Petrov" +EMAIL="ppetrov@paju.oulu.fi" |