academic/diamond: Added (A sequence aligner).

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

5 files changed, 161 insertions, 0 deletions

diff --git a/academic/diamond/README b/academic/diamond/README
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+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
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+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
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+++ b/academic/diamond/diamond.SlackBuild
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+#!/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
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+++ b/academic/diamond/diamond.info
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+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
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+++ b/academic/diamond/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------------------------------------------------------|
+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: