diff --git a/academic/amplicon/README b/academic/amplicon/README new file mode 100644 index 0000000000..395b56f031 --- /dev/null +++ b/academic/amplicon/README @@ -0,0 +1,10 @@ +Amplicon is a tool for designing PCR primers where groups of related +DNA sequences can be assessed in aligned form. Other useful features +that are not common in other PCR primer design software are handling +of gapped sequences and degenerate sites in aligned DNA. Amplicon can +import aligned DNA sequences produced by Clustal, or aligned +sequences in MEGA or Fasta format. + +For details and citation: +Jarman SN (2004) Amplicon: software for designing PCR primers on +aligned DNA sequences. Bioinformatics 20: 1644-1645. diff --git a/academic/amplicon/References b/academic/amplicon/References new file mode 100644 index 0000000000..cef68629d6 --- /dev/null +++ b/academic/amplicon/References @@ -0,0 +1,8 @@ +References + +Jarman SN (2004) Amplicon: software for designing PCR primers on aligned +DNA sequences. Bioinformatics 20: 1644-1645. + +Jarman SN, Deagle BE, Gales NJ (2004) Group-specific polymerase chain +reaction for DNA-based analysis of species diversity and identity in +dietary samples. Molecular Ecology 13: 1313-1322. diff --git a/academic/amplicon/amplicon.SlackBuild b/academic/amplicon/amplicon.SlackBuild new file mode 100644 index 0000000000..715746b531 --- /dev/null +++ b/academic/amplicon/amplicon.SlackBuild @@ -0,0 +1,51 @@ +#!/bin/sh + +# Slackware build script for amplicon +# Written by Petar Petrov, and +# hereby submitted to the public domain + +# THIS SLACKBUILD IS DISTRIBUTETD IN THE HOPE OF BEING +# USEFUL BUT WITHOUT ANY WARRANTY. THE AUTHOR IS _NOT_ +# RESPONSIBLE FOR ANY DAMAGE OR DATA LOSS CAUSED BY IT. + +PRGNAM=amplicon +VERSION=${VERSION:-b09.1} +ARCH=noarch +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +CWD=$(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 $PRGNAM-$VERSION +mkdir $PRGNAM-$VERSION +cd $PRGNAM-$VERSION +gunzip -c $CWD/Amplicon-Linux-$VERSION.py.gz > amplicon.py + +# Fix the window size +sed "s:root.maxsize(965,570):root.maxsize(1400,800):" -i amplicon.py + +install -D -m755 amplicon.py $PKG/usr/bin/amplicon.py + +# Manu item and icon +mkdir -p $PKG/usr/share/{applications,pixmaps} +cp $CWD/amplicon.desktop $PKG/usr/share/applications/ +cp $CWD/amplicon.png $PKG/usr/share/pixmaps + +mkdir -p $PKG/usr/doc/$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 +cat $CWD/doinst.sh > $PKG/install/doinst.sh + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} diff --git a/academic/amplicon/amplicon.desktop b/academic/amplicon/amplicon.desktop new file mode 100644 index 0000000000..7444f0c78a --- /dev/null +++ b/academic/amplicon/amplicon.desktop @@ -0,0 +1,7 @@ +[Desktop Entry] +Categories=Education; +Exec=python /usr/bin/amplicon.py +Icon=amplicon.png +Name=Amplicon +StartupNotify=false +Type=Application diff --git a/academic/amplicon/amplicon.info b/academic/amplicon/amplicon.info new file mode 100644 index 0000000000..baf1232189 --- /dev/null +++ b/academic/amplicon/amplicon.info @@ -0,0 +1,10 @@ +PRGNAM="amplicon" +VERSION="b09.1" +HOMEPAGE="http://amplicon.sourceforge.net/" +DOWNLOAD="http://downloads.sourceforge.net/amplicon/Amplicon-Linux-b09.1.py.gz" +MD5SUM="43e6bedbe16b7f423a88286910f8749a" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +MAINTAINER="Petar Petrov" +EMAIL="ppetrov@paju.oulu.fi" +APPROVED="Niels Horn" diff --git a/academic/amplicon/amplicon.png b/academic/amplicon/amplicon.png new file mode 100644 index 0000000000..d1fbd59445 Binary files /dev/null and b/academic/amplicon/amplicon.png differ diff --git a/academic/amplicon/doinst.sh b/academic/amplicon/doinst.sh new file mode 100644 index 0000000000..01ca62b341 --- /dev/null +++ b/academic/amplicon/doinst.sh @@ -0,0 +1,3 @@ +if [ -x /usr/bin/update-desktop-database ]; then + /usr/bin/update-desktop-database -q usr/share/applications >/dev/null 2>&1 +fi \ No newline at end of file diff --git a/academic/amplicon/slack-desc b/academic/amplicon/slack-desc new file mode 100644 index 0000000000..e3c789afa1 --- /dev/null +++ b/academic/amplicon/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 ':'. + + |-----handy-ruler------------------------------------------------------| +amplicon: amplicon (Design PCR primers on aligned sequences) +amplicon: +amplicon: Amplicon is a tool for designing PCR primers where groups of related +amplicon: DNA sequences can be assessed in aligned form. This is especially +amplicon: useful for designing 'group-specific' PCR primer sets that produce +amplicon: amplicons from a targer group of species, but not from other groups +amplicon: of species. +amplicon: +amplicon: +amplicon: References: /usr/doc/amplicon-$VERSION/References +amplicon: Home: http://amplicon.sourceforge.net/