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| -rw-r--r-- | academic/ncbi-blast-plus/README | 17 | ||||
| -rw-r--r-- | academic/ncbi-blast-plus/References | 8 | ||||
| -rw-r--r-- | academic/ncbi-blast-plus/ncbi-blast-plus.SlackBuild | 115 | ||||
| -rw-r--r-- | academic/ncbi-blast-plus/ncbi-blast-plus.info | 10 | ||||
| -rw-r--r-- | academic/ncbi-blast-plus/slack-desc | 19 |
5 files changed, 169 insertions, 0 deletions
diff --git a/academic/ncbi-blast-plus/README b/academic/ncbi-blast-plus/README new file mode 100644 index 0000000000000..0aeda537eb8d2 --- /dev/null +++ b/academic/ncbi-blast-plus/README @@ -0,0 +1,17 @@ +BLAST+ Command Line Applications + +The NCBI Basic Local Alignment Search Tool (BLAST) finds regions of +local similarity between sequences. The program compares nucleotide or +protein sequences to sequence databases and calculates the statistical +significance of matches. BLAST can be used to infer functional and +evolutionary relationships between sequences as well as help identify +members of gene families. + +BLAST+ is a new suite of BLAST tools that utilizes the NCBI C++ +Toolkit. The BLAST+ applications have a number of performance and +feature improvements over the legacy BLAST applications (ncbi-blast). + +For details and citation, please see the BLAST+ user manual from the +program's web site and the article in BMC Bioinformatics. + +This just repackages the binaries provided from upstream. diff --git a/academic/ncbi-blast-plus/References b/academic/ncbi-blast-plus/References new file mode 100644 index 0000000000000..dfe6000c14002 --- /dev/null +++ b/academic/ncbi-blast-plus/References @@ -0,0 +1,8 @@ +BLAST® Help [Internet]. Bethesda (MD): National Center for +Biotechnology Information (US); 2008-. Available from: +http://www.ncbi.nlm.nih.gov/books/NBK1762/ + +BMC Bioinformatics. 2009 Dec 15;10:421. +BLAST+: architecture and applications. +Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL. +Source diff --git a/academic/ncbi-blast-plus/ncbi-blast-plus.SlackBuild b/academic/ncbi-blast-plus/ncbi-blast-plus.SlackBuild new file mode 100644 index 0000000000000..c3a677bdadaaf --- /dev/null +++ b/academic/ncbi-blast-plus/ncbi-blast-plus.SlackBuild @@ -0,0 +1,115 @@ +#!/bin/sh + +# Slackware build script for ncbi-blast-plus + +# 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=ncbi-blast-plus +VERSION=${VERSION:-2.2.27} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +SRCNAM=ncbi-blast +SRCVER=2.2.27+ + +if [ -z "$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 + +# Determine the source arch +if [ "$ARCH" = "x86_64" ]; then + SRCARCH="x64" +else + SRCARCH="ia32" +fi + +# Construct the tarball name +TARNAME=$SRCNAM-$SRCVER-$SRCARCH-linux + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $SRCNAM-$SRCVER +tar xvf $CWD/$TARNAME.tar.gz +cd $SRCNAM-$SRCVER +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. +cd bin +install -D -m755 blast_formatter $PKG/usr/bin/blast_formatter +install -D -m755 blastdb_aliastool $PKG/usr/bin/blastdb_aliastool +install -D -m755 blastdbcheck $PKG/usr/bin/blastdbcheck +install -D -m755 blastdbcmd $PKG/usr/bin/blastdbcmd +install -D -m755 blastn $PKG/usr/bin/blastn +install -D -m755 blastp $PKG/usr/bin/blastp +install -D -m755 blastx $PKG/usr/bin/blastx +install -D -m755 convert2blastmask $PKG/usr/bin/convert2blastmask +install -D -m755 deltablast $PKG/usr/bin/deltablast +install -D -m755 dustmasker $PKG/usr/bin/dustmasker +install -D -m755 legacy_blast.pl $PKG/usr/bin/legacy_blast.pl +install -D -m755 makeblastdb $PKG/usr/bin/makeblastdb +install -D -m755 makembindex $PKG/usr/bin/makembindex +install -D -m755 makeprofiledb $PKG/usr/bin/makeprofiledb +install -D -m755 psiblast $PKG/usr/bin/psiblast +install -D -m755 rpsblast $PKG/usr/bin/rpsblast +install -D -m755 rpstblastn $PKG/usr/bin/rpstblastn +install -D -m755 segmasker $PKG/usr/bin/segmasker +install -D -m755 tblastn $PKG/usr/bin/tblastn +install -D -m755 tblastx $PKG/usr/bin/tblastx +install -D -m755 update_blastdb.pl $PKG/usr/bin/update_blastdb.pl +install -D -m755 windowmasker $PKG/usr/bin/windowmasker +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 \ + ChangeLog LICENSE README \ + $PKG/usr/doc/$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.${PKGTYPE:-tgz} diff --git a/academic/ncbi-blast-plus/ncbi-blast-plus.info b/academic/ncbi-blast-plus/ncbi-blast-plus.info new file mode 100644 index 0000000000000..c4c47d45d902c --- /dev/null +++ b/academic/ncbi-blast-plus/ncbi-blast-plus.info @@ -0,0 +1,10 @@ +PRGNAM="ncbi-blast-plus" +VERSION="2.2.27" +HOMEPAGE="http://blast.ncbi.nlm.nih.gov/" +DOWNLOAD="ftp://ftp.ncbi.nih.gov/blast/executables/blast+/2.2.27/ncbi-blast-2.2.27+-ia32-linux.tar.gz" +MD5SUM="8e22b1f2fe816e2f8812dcf3a5980bff" +DOWNLOAD_x86_64="ftp://ftp.ncbi.nih.gov/blast/executables/blast+/2.2.27/ncbi-blast-2.2.27+-x64-linux.tar.gz" +MD5SUM_x86_64="905d308507392cd86bbe701839b0a601" +REQUIRES="" +MAINTAINER="Petar Petrov" +EMAIL="ppetrov@paju.oulu.fi" diff --git a/academic/ncbi-blast-plus/slack-desc b/academic/ncbi-blast-plus/slack-desc new file mode 100644 index 0000000000000..c698328a33343 --- /dev/null +++ b/academic/ncbi-blast-plus/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +ncbi-blast-plus: ncbi-blast-plus: (BLAST+ Command Line Applications) +ncbi-blast-plus: +ncbi-blast-plus: BLAST+ is a new suite of BLAST tools that utilizes the NCBI C++ +ncbi-blast-plus: Toolkit. The BLAST+ applications have a number of performance and +ncbi-blast-plus: feature improvements over the legacy BLAST applications (ncbi-blast). +ncbi-blast-plus: +ncbi-blast-plus: Home: http://blast.ncbi.nlm.nih.gov/ +ncbi-blast-plus: References: /usr/doc/ncbi-blast-plus-$VERSION/References +ncbi-blast-plus: +ncbi-blast-plus: +ncbi-blast-plus: |