academic/ncbi-blast+: Added (BLAST+ Command Line Applications).

Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>

5 files changed, 189 insertions, 0 deletions

diff --git a/academic/ncbi-blast+/README b/academic/ncbi-blast+/README
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+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.
+
+The Basic Local Alignment Search Tool (BLAST) is the most widely used
+sequence similarity tool. There are versions of BLAST that compare
+protein queries to protein databases, nucleotide queries to nucleotide
+databases, as well as versions that translate nucleotide queries or
+databases in all six frames and compare to protein databases or queries.
+PSI-BLAST produces a position-specific-scoring-matrix (PSSM) starting
+with a protein query, and then uses that PSSM to perform further
+searches. It is also possible to compare a protein or nucleotide query
+to a database of PSSM’s. The NCBI supports a BLAST web page (at
+blast.ncbi.nlm.nih.gov) as well as a network service. The NCBI also
+distributes stand-alone BLAST applications for users who wish to run
+BLAST on their own machines or with their own databases.
+
+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).
+
+Some useful links:
+
+Help https://www.ncbi.nlm.nih.gov/books/NBK1762/
+Manual https://www.ncbi.nlm.nih.gov/books/NBK279690/
+Downloads ftp://ftp.ncbi.nih.gov/blast/executables/blast+/
+Databases ftp://ftp.ncbi.nlm.nih.gov/blast/db/
+ChangeLog http://www.ncbi.nlm.nih.gov/books/NBK131777
+Reference https://www.ncbi.nlm.nih.gov/pubmed/20003500
+
+Citing:
+BLAST+: architecture and applications. Camacho C, Coulouris G, Avagyan
+V, Ma N, Papadopoulos J, Bealer K, Madden TL. BMC Bioinformatics. 2009
+Dec 15;10:421. doi: 10.1186/1471-2105-10-421.
diff --git a/academic/ncbi-blast+/References b/academic/ncbi-blast+/References
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+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+/ncbi-blast+.SlackBuild b/academic/ncbi-blast+/ncbi-blast+.SlackBuild
new file mode 100644
index 0000000000000..1e6757bc0d62a
--- /dev/null
+++ b/academic/ncbi-blast+/ncbi-blast+.SlackBuild
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+#!/bin/sh
+
+# Slackware build script for ncbi-blast+
+# This takes the place of ncbi-blast-plus (2013-2018), which just
+# repackaged the binaries provided by upstream.
+
+# 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+
+DIRNAM=ncbi-blast
+VERSION=${VERSION:-2.7.1}
+BUILD=${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" = "i586" ]; then
+  SLKCFLAGS="-O2 -march=i586 -mtune=i686"
+  LIBDIRSUFFIX=""
+elif [ "$ARCH" = "i686" ]; then
+  SLKCFLAGS="-O2 -march=i686 -mtune=i686"
+  LIBDIRSUFFIX=""
+elif [ "$ARCH" = "x86_64" ]; then
+  SLKCFLAGS="-O2 -fPIC"
+  LIBDIRSUFFIX="64"
+else
+  SLKCFLAGS="-O2"
+  LIBDIRSUFFIX=""
+fi
+
+set -e
+
+rm -rf $PKG
+mkdir -p $TMP $PKG $OUTPUT
+cd $TMP
+rm -rf ${DIRNAM}-${VERSION}+-src
+tar xvf $CWD/${DIRNAM}-${VERSION}+-src.tar.gz
+cd ${DIRNAM}-${VERSION}+-src
+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 {} \;
+
+cd c++
+
+# NOTE! Some additional options we could consider are:
+# --without-autodep \              # automatic generation of dependencies (GNU make)
+# --without-makefile-auto-update \ # do not auto-update generated makefiles
+# --without-caution \              # proceed without asking when in doubt
+# --without-boost \                # do not use Boost
+# The full list of options is available in c++/src/build-system/configure
+
+CFLAGS="$SLKCFLAGS" \
+CXXFLAGS="$SLKCFLAGS" \
+./configure \
+  --prefix=/usr \
+  --libdir=/usr/lib${LIBDIRSUFFIX} \
+  --sysconfdir=/etc \
+  --localstatedir=/var \
+  --mandir=/usr/man \
+  --docdir=/usr/doc/$PRGNAM-$VERSION \
+  --with-dll \
+  --with-mt \
+  --without-debug \
+  --without-downloaded-vdb \
+  --without-bdb \
+  --build=$ARCH-slackware-linux
+
+make
+make prefix=$PKG/usr install 
+
+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
+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+/ncbi-blast+.info b/academic/ncbi-blast+/ncbi-blast+.info
new file mode 100644
index 0000000000000..78639eac62d40
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+++ b/academic/ncbi-blast+/ncbi-blast+.info
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+PRGNAM="ncbi-blast+"
+VERSION="2.7.1"
+HOMEPAGE="https://blast.ncbi.nlm.nih.gov/"
+DOWNLOAD="ftp://ftp.ncbi.nih.gov/blast/executables/blast+/2.7.1/ncbi-blast-2.7.1+-src.tar.gz"
+MD5SUM="48b37565cf5f3d17388daaf0f17b95bc"
+DOWNLOAD_x86_64=""
+MD5SUM_x86_64=""
+REQUIRES="lmdb"
+MAINTAINER="Petar Petrov"
+EMAIL="slackalaxy@gmail.com"
diff --git a/academic/ncbi-blast+/slack-desc b/academic/ncbi-blast+/slack-desc
new file mode 100644
index 0000000000000..354278ce9ee34
--- /dev/null
+++ b/academic/ncbi-blast+/slack-desc
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+# 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+: ncbi-blast+ (BLAST+ Command Line Applications)
+ncbi-blast+:
+ncbi-blast+: BLAST+ is a new suite of BLAST tools that utilizes the NCBI C++
+ncbi-blast+: Toolkit. The BLAST+ applications have a number of performance and
+ncbi-blast+: feature improvements over the legacy BLAST applications (ncbi-blast).
+ncbi-blast+:
+ncbi-blast+: Home: https://blast.ncbi.nlm.nih.gov/
+ncbi-blast+: Databases: ftp://ftp.ncbi.nlm.nih.gov/blast/db/
+ncbi-blast+: ChangeLog: http://www.ncbi.nlm.nih.gov/books/NBK131777
+ncbi-blast+: Manual: https://www.ncbi.nlm.nih.gov/books/NBK279690/
+ncbi-blast+: Help: https://www.ncbi.nlm.nih.gov/books/NBK1762/