From baca6beb0c818a6727efd6b1e5b9552928bcc6a9 Mon Sep 17 00:00:00 2001 From: Petar Petrov Date: Sun, 27 Nov 2016 00:12:08 +0000 Subject: academic/HMMER: Added (biosequence analysis). Signed-off-by: David Spencer --- academic/HMMER/HMMER.SlackBuild | 108 ++++++++++++++++++++++++++++++++++++++++ academic/HMMER/HMMER.info | 10 ++++ academic/HMMER/README | 19 +++++++ academic/HMMER/slack-desc | 19 +++++++ 4 files changed, 156 insertions(+) create mode 100644 academic/HMMER/HMMER.SlackBuild create mode 100644 academic/HMMER/HMMER.info create mode 100644 academic/HMMER/README create mode 100644 academic/HMMER/slack-desc (limited to 'academic') diff --git a/academic/HMMER/HMMER.SlackBuild b/academic/HMMER/HMMER.SlackBuild new file mode 100644 index 0000000000000..ed7b38faeb32d --- /dev/null +++ b/academic/HMMER/HMMER.SlackBuild @@ -0,0 +1,108 @@ +#!/bin/sh + +# Slackware build script for HMMER + +# Copyright 2016 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=HMMER +SRCNAM=hmmer +VERSION=${VERSION:-3.1b2} +BUILD=${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 $SRCNAM-$VERSION +tar xvf $CWD/$SRCNAM-$VERSION.tar.gz +cd $SRCNAM-$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 {} \; + +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +./configure \ + --prefix=/usr \ + --libdir=/usr/lib${LIBDIRSUFFIX} \ + --sysconfdir=/etc \ + --localstatedir=/var \ + --mandir=/usr/man \ + --docdir=/usr/doc/$PRGNAM-$VERSION \ + --build=$ARCH-slackware-linux + +make +make check +make install DESTDIR=$PKG + +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 + +find $PKG/usr/man -type f -exec gzip -9 {} \; +for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done + +# Include some tutorial examples +mkdir -p $PKG/usr/share/$PRGNAM +cp -a tutorial/* $PKG/usr/share/$PRGNAM + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + INSTALL LICENSE README release-notes Userguide.pdf \ + $PKG/usr/doc/$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/HMMER/HMMER.info b/academic/HMMER/HMMER.info new file mode 100644 index 0000000000000..e05cab2782a27 --- /dev/null +++ b/academic/HMMER/HMMER.info @@ -0,0 +1,10 @@ +PRGNAM="HMMER" +VERSION="3.1b2" +HOMEPAGE="http://hmmer.org/" +DOWNLOAD="http://eddylab.org/software/hmmer3/3.1b2/hmmer-3.1b2.tar.gz" +MD5SUM="c8c141018bc0ccd7fc37b33f2b945d5f" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/HMMER/README b/academic/HMMER/README new file mode 100644 index 0000000000000..7129424d65512 --- /dev/null +++ b/academic/HMMER/README @@ -0,0 +1,19 @@ +HMMER: biosequence analysis using profile hidden Markov models + +HMMER is used for searching sequence databases for sequence homologs, +and for making sequence alignments. It implements methods using +probabilistic models called profile hidden Markov models (profile HMMs). + +HMMER is often used together with a profile database, such as Pfam or +many of the databases that participate in Interpro. But HMMER can also +work with query sequences, not just profiles, just like BLAST. For +example, you can search a protein query sequence against a database with +phmmer, or do an iterative search with jackhmmer. + +HMMER is designed to detect remote homologs as sensitively as possible, +relying on the strength of its underlying probability models. In the +past, this strength came at significant computational expense, but as +of the new HMMER3 project, HMMER is now essentially as fast as BLAST. + +Publications: +http://hmmer.org/publications.html diff --git a/academic/HMMER/slack-desc b/academic/HMMER/slack-desc new file mode 100644 index 0000000000000..a14f68d22cc57 --- /dev/null +++ b/academic/HMMER/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------------------------------------------------------| +HMMER: HMMER (Biosequence analysis using profile hidden Markov models) +HMMER: +HMMER: HMMER is used for searching sequence databases for sequence +HMMER: homologs, and for making sequence alignments. It implements +HMMER: methods using probabilistic models called profile hidden Markov +HMMER: models (profile HMMs). +HMMER: +HMMER: Home: http://hmmer.org/ +HMMER: Publications: http://hmmer.org/publications.html +HMMER: +HMMER: -- cgit v1.2.3