diff options
Diffstat (limited to 'academic')
-rw-r--r-- | academic/ncbi-rmblastn/README | 13 | ||||
-rw-r--r-- | academic/ncbi-rmblastn/ncbi-rmblastn.SlackBuild | 80 | ||||
-rw-r--r-- | academic/ncbi-rmblastn/ncbi-rmblastn.info | 10 | ||||
-rw-r--r-- | academic/ncbi-rmblastn/slack-desc | 19 |
4 files changed, 122 insertions, 0 deletions
diff --git a/academic/ncbi-rmblastn/README b/academic/ncbi-rmblastn/README new file mode 100644 index 0000000000..b203d952fa --- /dev/null +++ b/academic/ncbi-rmblastn/README @@ -0,0 +1,13 @@ +RMBlast is a RepeatMasker compatible version of the standard NCBI BLAST +suite. The primary difference between this distribution and the NCBI +distribution is the addition of a new program "rmblastn" for use with +RepeatMasker and RepeatModeler. + +RMBlast supports RepeatMasker searches by adding a few necessary +features to the stock NCBI blastn program. These include: + +- Support for custom matrices ( without KA-Statistics ) +- Support for cross_match-like complexity adjusted scoring + (Cross_match is Phil Green's seeded smith-waterman search algorithm: + www.phrap.org ) +- Support for cross_match-like masklevel filtering. diff --git a/academic/ncbi-rmblastn/ncbi-rmblastn.SlackBuild b/academic/ncbi-rmblastn/ncbi-rmblastn.SlackBuild new file mode 100644 index 0000000000..b78a2be545 --- /dev/null +++ b/academic/ncbi-rmblastn/ncbi-rmblastn.SlackBuild @@ -0,0 +1,80 @@ +#!/bin/sh + +# Slackware build script for ncbi-rmblastn + +# 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=ncbi-rmblastn +VERSION=${VERSION:-2.2.28} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +if [ -z "$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=${OUTPUT:-/tmp} + +set -e + +# Determine the binary arch +if [ "$ARCH" = "x86_64" ]; then + BINARCH="x64" +else + BINARCH="ia32" +fi + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION-$BINARCH-linux.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 {} \; + +cd bin +install -D -m755 rmblastn $PKG/usr/bin/rmblastn +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 LICENSE README $PKG/usr/doc/$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-rmblastn/ncbi-rmblastn.info b/academic/ncbi-rmblastn/ncbi-rmblastn.info new file mode 100644 index 0000000000..b1daee632b --- /dev/null +++ b/academic/ncbi-rmblastn/ncbi-rmblastn.info @@ -0,0 +1,10 @@ +PRGNAM="ncbi-rmblastn" +VERSION="2.2.28" +HOMEPAGE="ftp://ftp.ncbi.nlm.nih.gov/blast/executables/rmblast/" +DOWNLOAD="ftp://ftp.ncbi.nlm.nih.gov/blast/executables/rmblast/2.2.28/ncbi-rmblastn-2.2.28-ia32-linux.tar.gz" +MD5SUM="9e78451a710b668d81e5cd8573fa7303" +DOWNLOAD_x86_64="ftp://ftp.ncbi.nlm.nih.gov/blast/executables/rmblast/2.2.28/ncbi-rmblastn-2.2.28-x64-linux.tar.gz" +MD5SUM_x86_64="b668b3c5869cd7cdde5d44463c8417f9" +REQUIRES="ncbi-blast-plus" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/ncbi-rmblastn/slack-desc b/academic/ncbi-rmblastn/slack-desc new file mode 100644 index 0000000000..f3a664b73d --- /dev/null +++ b/academic/ncbi-rmblastn/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------------------------------------------------------| +ncbi-rmblastn: ncbi-rmblastn (NCBI RMBlast) +ncbi-rmblastn: +ncbi-rmblastn: RMBlast supports RepeatMasker searches by adding a few necessary +ncbi-rmblastn: features to the stock NCBI blastn program. These include: +ncbi-rmblastn: +ncbi-rmblastn: Support for custom matrices ( without KA-Statistics ) +ncbi-rmblastn: Support for cross_match-like complexity adjusted scoring +ncbi-rmblastn: Support for cross_match-like masklevel filtering +ncbi-rmblastn: +ncbi-rmblastn: +ncbi-rmblastn: |