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author Willy Sudiarto Raharjo <willysr@slackbuilds.org>2018-12-24 19:48:46 +0700
committer Willy Sudiarto Raharjo <willysr@slackbuilds.org>2018-12-24 22:16:57 +0700
commit98f0d763327d6f3bd345fc697e2688dc279c91d2 (patch)
treea9236705a5a8b61c0419777cab8bceeb4186421b /academic
parentf0c4d5692eff72db7e278782b635c85b0a3de42a (diff)
downloadslackbuilds-98f0d763327d6f3bd345fc697e2688dc279c91d2.tar.gz
slackbuilds-98f0d763327d6f3bd345fc697e2688dc279c91d2.tar.xz
academic/ncbi-blast-plus: Removed (Use ncbi-blast+).
Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>
Diffstat (limited to 'academic')
-rw-r--r--academic/ncbi-blast-plus/README23
-rw-r--r--academic/ncbi-blast-plus/References8
-rw-r--r--academic/ncbi-blast-plus/ncbi-blast-plus.SlackBuild118
-rw-r--r--academic/ncbi-blast-plus/ncbi-blast-plus.info10
-rw-r--r--academic/ncbi-blast-plus/slack-desc19
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: