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Diffstat (limited to 'academic/pal2nal')
-rw-r--r-- | academic/pal2nal/README | 17 | ||||
-rw-r--r-- | academic/pal2nal/References | 5 | ||||
-rw-r--r-- | academic/pal2nal/pal2nal.SlackBuild | 68 | ||||
-rw-r--r-- | academic/pal2nal/pal2nal.info | 10 | ||||
-rw-r--r-- | academic/pal2nal/slack-desc | 19 |
5 files changed, 119 insertions, 0 deletions
diff --git a/academic/pal2nal/README b/academic/pal2nal/README new file mode 100644 index 0000000000000..db752e12bcb40 --- /dev/null +++ b/academic/pal2nal/README @@ -0,0 +1,17 @@ +PAL2NAL is a program that converts a multiple sequence alignment of +proteins and the corresponding DNA (or mRNA) sequences into a codon- +based DNA alignment. The program automatically assigns the corresponding +codon sequence even if the input DNA sequence has mismatches with the +input protein sequence, or contains UTRs,polyA tails. It can also deal +with frame shifts in the input alignment, which is suitable for the +analysis of pseudogenes. + +The resulting codon-based DNA alignment can further be subjected to the +calculation of synonymous (Ks) and non-synonymous (Ka) substitution +rates. + +If you use PAL2NAL, please cite the following paper: + +Mikita Suyama, David Torrents, and Peer Bork (2006) +PAL2NAL: robust conversion of protein sequence alignment into the +corresponding codon alignments. Nucleic Acids Res. 34:W609-W612. diff --git a/academic/pal2nal/References b/academic/pal2nal/References new file mode 100644 index 0000000000000..1e5ad383abf75 --- /dev/null +++ b/academic/pal2nal/References @@ -0,0 +1,5 @@ +If you use PAL2NAL, please cite the following paper: + +Mikita Suyama, David Torrents, and Peer Bork (2006) +PAL2NAL: robust conversion of protein sequence alignment into the +corresponding codon alignments. Nucleic Acids Res. 34:W609-W612 diff --git a/academic/pal2nal/pal2nal.SlackBuild b/academic/pal2nal/pal2nal.SlackBuild new file mode 100644 index 0000000000000..86464650eb8c0 --- /dev/null +++ b/academic/pal2nal/pal2nal.SlackBuild @@ -0,0 +1,68 @@ +#!/bin/sh + +# Slackware build script for pal2nal + +# Copyright 2017 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=pal2nal +VERSION=${VERSION:-14.0} +SRCVER=v14 +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +ARCH=noarch + +CWD=$(pwd) +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf ${PRGNAM}.${SRCVER} +tar xvf $CWD/${PRGNAM}.${SRCVER}.tar.gz +cd ${PRGNAM}.${SRCVER} +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 {} \; + +install -D -m755 $PRGNAM.pl $PKG/usr/bin/$PRGNAM.pl + +# Copy some examples +mkdir -p $PKG/usr/share/$PRGNAM +cp -a for_paml test.aln test.nuc $PKG/usr/share/$PRGNAM + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a README $PKG/usr/doc/$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/pal2nal/pal2nal.info b/academic/pal2nal/pal2nal.info new file mode 100644 index 0000000000000..ded794e81b4bc --- /dev/null +++ b/academic/pal2nal/pal2nal.info @@ -0,0 +1,10 @@ +PRGNAM="pal2nal" +VERSION="14.0" +HOMEPAGE="http://www.bork.embl.de/pal2nal/" +DOWNLOAD="http://www.bork.embl.de/pal2nal/distribution/pal2nal.v14.tar.gz" +MD5SUM="cf8b2b9aaa7dce740a81454cf8136ba1" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/pal2nal/slack-desc b/academic/pal2nal/slack-desc new file mode 100644 index 0000000000000..ab69b395e2f2b --- /dev/null +++ b/academic/pal2nal/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------------------------------------------------------| +pal2nal: pal2nal (Create a codon-based DNA alignment) +pal2nal: +pal2nal: PAL2NAL is a program that converts a multiple sequence alignment +pal2nal: of proteins and the corresponding DNA (or mRNA) sequences into +pal2nal: a codon-based DNA alignment. The resulting codon-based DNA +pal2nal: alignment can further be subjected to the calculation of +pal2nal: synonymous (Ks) and non-synonymous (Ka) substitution rates. +pal2nal: +pal2nal: References: /usr/doc/pal2nal-14.0/References +pal2nal: Home: http://www.bork.embl.de/pal2nal/ +pal2nal: |