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| -rw-r--r-- | academic/ncbi-blast-plus/README | 23 | ||||
| -rw-r--r-- | academic/ncbi-blast-plus/References | 8 | ||||
| -rw-r--r-- | academic/ncbi-blast-plus/ncbi-blast-plus.SlackBuild | 118 | ||||
| -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, 0 insertions, 178 deletions
diff --git a/academic/ncbi-blast-plus/README b/academic/ncbi-blast-plus/README deleted file mode 100644 index d890a704c0..0000000000 --- a/academic/ncbi-blast-plus/README +++ /dev/null @@ -1,23 +0,0 @@ -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. - -NOTE ABOUT x86: -Since version 2.2.31, NCBI does not provide 32-bit executables of -BLAST+ for Linux. Their reasoning is that the limited memory and -processing power of 32-bit systems is not suitable for the large -databases searched by BLAST. diff --git a/academic/ncbi-blast-plus/References b/academic/ncbi-blast-plus/References deleted file mode 100644 index dfe6000c14..0000000000 --- a/academic/ncbi-blast-plus/References +++ /dev/null @@ -1,8 +0,0 @@ -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 deleted file mode 100644 index eb2cb67f33..0000000000 --- a/academic/ncbi-blast-plus/ncbi-blast-plus.SlackBuild +++ /dev/null @@ -1,118 +0,0 @@ -#!/bin/sh - -# Slackware build script for ncbi-blast-plus - -# Copyright 2013-2018 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=ncbi-blast-plus -VERSION=${VERSION:-2.7.1} -BUILD=${BUILD:-1} -TAG=${TAG:-_SBo} - -SRCNAM=ncbi-blast -SRCVER=2.7.1+ - -if [ -z "$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=${OUTPUT:-/tmp} - -set -e - -# Check for host architecture. Distribution of 32bit binaries has been -# dropped from NCBI. For more information, please read: -# http://www.ncbi.nlm.nih.gov/mailman/pipermail/blast-announce/2015q2/000112.html -if [ "$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 -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 {} \; - -# 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 doc/README.txt \ - $PKG/usr/doc/$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 deleted file mode 100644 index 45cdb1abf2..0000000000 --- a/academic/ncbi-blast-plus/ncbi-blast-plus.info +++ /dev/null @@ -1,10 +0,0 @@ -PRGNAM="ncbi-blast-plus" -VERSION="2.7.1" -HOMEPAGE="https://blast.ncbi.nlm.nih.gov/" -DOWNLOAD="UNSUPPORTED" -MD5SUM="" -DOWNLOAD_x86_64="ftp://ftp.ncbi.nih.gov/blast/executables/blast+/2.7.1/ncbi-blast-2.7.1+-x64-linux.tar.gz" -MD5SUM_x86_64="9d31dff42ab2b0d9565f761ce340e4ba" -REQUIRES="" -MAINTAINER="Petar Petrov" -EMAIL="slackalaxy@gmail.com" diff --git a/academic/ncbi-blast-plus/slack-desc b/academic/ncbi-blast-plus/slack-desc deleted file mode 100644 index 75bb9a6dbe..0000000000 --- a/academic/ncbi-blast-plus/slack-desc +++ /dev/null @@ -1,19 +0,0 @@ -# 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: https://blast.ncbi.nlm.nih.gov/ -ncbi-blast-plus: -ncbi-blast-plus: -ncbi-blast-plus: -ncbi-blast-plus: |