From 5a3aecffdca70b25e44a246ed1b601b01a6674d8 Mon Sep 17 00:00:00 2001 From: Petar Petrov Date: Mon, 24 Dec 2018 09:11:11 +0700 Subject: academic/diamond: Added (A sequence aligner). Signed-off-by: Willy Sudiarto Raharjo --- academic/diamond/README | 33 +++++++++++++ academic/diamond/References | 2 + academic/diamond/diamond.SlackBuild | 97 +++++++++++++++++++++++++++++++++++++ academic/diamond/diamond.info | 10 ++++ academic/diamond/slack-desc | 19 ++++++++ 5 files changed, 161 insertions(+) create mode 100644 academic/diamond/README create mode 100644 academic/diamond/References create mode 100644 academic/diamond/diamond.SlackBuild create mode 100644 academic/diamond/diamond.info create mode 100644 academic/diamond/slack-desc (limited to 'academic') diff --git a/academic/diamond/README b/academic/diamond/README new file mode 100644 index 0000000000..a5c66d0988 --- /dev/null +++ b/academic/diamond/README @@ -0,0 +1,33 @@ +DIAMOND is a sequence aligner for protein and translated DNA searches, +designed for high performance analysis of big sequence data. The key +features are: + +- Pairwise alignment of proteins and translated DNA at 500x-20,000x + speed of BLAST. +- Frameshift alignments for long read analysis. +- Low resource requirements and suitable for running on standard + desktops or laptops. +- Various output formats, including BLAST pairwise, tabular and XML, + as well as taxonomic classification. + +To now run an alignment task, we assume to have a protein database file +in FASTA format named `nr.faa` and a file of DNA reads that we want to +align named `reads.fna`. + +In order to set up a reference database for DIAMOND, the `makedb` +command needs to be executed with the following command line: + + $ diamond makedb --in nr.faa -d nr + +This will create a binary DIAMOND database file with the specified name +(`nr.dmnd`). The alignment task may then be initiated using the `blastx` +command like this: + + $ diamond blastx -d nr -q reads.fna -o matches.m8 + +The output file here is specified with the `–o` option and named +`matches.m8`. By default, it is generated in BLAST tabular format. + +Publication: +Buchfink B, Xie C, Huson DH, "Fast and sensitive protein alignment using +DIAMOND", Nature Methods 12, 59-60 (2015). doi:10.1038/nmeth.3176 diff --git a/academic/diamond/References b/academic/diamond/References new file mode 100644 index 0000000000..9eca810bbc --- /dev/null +++ b/academic/diamond/References @@ -0,0 +1,2 @@ +Buchfink B, Xie C, Huson DH, "Fast and sensitive protein alignment using +DIAMOND", Nature Methods 12, 59-60 (2015). doi:10.1038/nmeth.3176 diff --git a/academic/diamond/diamond.SlackBuild b/academic/diamond/diamond.SlackBuild new file mode 100644 index 0000000000..934c1e800a --- /dev/null +++ b/academic/diamond/diamond.SlackBuild @@ -0,0 +1,97 @@ +#!/bin/sh + +# Slackware build script for diamond + +# Copyright 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=diamond +VERSION=${VERSION:-0.9.23} +BUILD=${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 $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION +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 {} \; + +mkdir -p build +cd build + cmake \ + -DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_INSTALL_PREFIX=/usr \ + -DCMAKE_BUILD_TYPE=Release .. + make + make install DESTDIR=$PKG +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 \ + ${PRGNAM}_manual.pdf LICENSE README.md src/ChangeLog \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References + +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/diamond/diamond.info b/academic/diamond/diamond.info new file mode 100644 index 0000000000..5163768da2 --- /dev/null +++ b/academic/diamond/diamond.info @@ -0,0 +1,10 @@ +PRGNAM="diamond" +VERSION="0.9.23" +HOMEPAGE="https://github.com/bbuchfink/diamond" +DOWNLOAD="https://github.com/bbuchfink/diamond/archive/v0.9.23/diamond-0.9.23.tar.gz" +MD5SUM="3597695081d4b6fd8978c257cdb5fe4a" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/diamond/slack-desc b/academic/diamond/slack-desc new file mode 100644 index 0000000000..d94b799c57 --- /dev/null +++ b/academic/diamond/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------------------------------------------------------| +diamond: diamond (A sequence aligner for protein and translated DNA) +diamond: +diamond: DIAMOND is a sequence aligner for protein and translated DNA +diamond: searches, designed for high performance analysis of big sequence +diamond: data. The key features are: +diamond: +diamond: 1) 500x-20,000x speed of BLAST +diamond: 2) Frameshift alignments for long read analysis. +diamond: 3) Low resource requirements +diamond: 4) Various output formats +diamond: -- cgit v1.2.3-65-gdbad