From f82ed85b019ac2ef2166beaf031a2d32947f3011 Mon Sep 17 00:00:00 2001 From: Petar Petrov Date: Sun, 4 Sep 2011 12:59:26 -0300 Subject: academic/perlprimer: Added (Design primers for PCR and sequencing) Signed-off-by: Niels Horn --- academic/perlprimer/README | 26 ++++++++++++++++ academic/perlprimer/References | 5 +++ academic/perlprimer/doinst.sh | 3 ++ academic/perlprimer/perlprimer.SlackBuild | 50 ++++++++++++++++++++++++++++++ academic/perlprimer/perlprimer.desktop | 7 +++++ academic/perlprimer/perlprimer.info | 10 ++++++ academic/perlprimer/perlprimer.png | Bin 0 -> 4909 bytes academic/perlprimer/slack-desc | 19 ++++++++++++ 8 files changed, 120 insertions(+) create mode 100644 academic/perlprimer/README create mode 100644 academic/perlprimer/References create mode 100644 academic/perlprimer/doinst.sh create mode 100644 academic/perlprimer/perlprimer.SlackBuild create mode 100644 academic/perlprimer/perlprimer.desktop create mode 100644 academic/perlprimer/perlprimer.info create mode 100644 academic/perlprimer/perlprimer.png create mode 100644 academic/perlprimer/slack-desc (limited to 'academic') diff --git a/academic/perlprimer/README b/academic/perlprimer/README new file mode 100644 index 0000000000..12917e35e9 --- /dev/null +++ b/academic/perlprimer/README @@ -0,0 +1,26 @@ +PerlPrimer is a free, open-source GUI application written in Perl +that designs primers for standard PCR, bisulphite PCR, real-time PCR +(QPCR) and sequencing. It aims to automate and simplify the process +of primer design. + +PerlPrimer's current features include the following: + +- Calculation of possible primer-dimers +- Retrieval of genomic or cDNA sequences from Ensembl (including both + sequences automatically for QPCR) +- Ability to BLAST search primers using the NCBI server or a local + server +- Results can be saved or optionally exported in a tab-delimited + format that is compatible with most spreadsheet applications. +- ORF and CpG island detection algorithms +- Ability to add cloning sequences to primers, automatically adjusted + to be in-frame +- QPCR primer design without manual intron-exon boundary entry + +For details and citation: +Marshall OJ. PerlPrimer: cross-platform, graphical primer design for +standard, bisulphite and real-time PCR. Bioinformatics 2004 +20(15):2471-2472 + +This requires perl-tk and libwww-perl. +For Real Time PCR, spidey is required. diff --git a/academic/perlprimer/References b/academic/perlprimer/References new file mode 100644 index 0000000000..730eab0e32 --- /dev/null +++ b/academic/perlprimer/References @@ -0,0 +1,5 @@ +References + +Marshall OJ. PerlPrimer: cross-platform, graphical primer design +for standard, bisulphite and real-time PCR. Bioinformatics 2004 +20(15):2471-2472 diff --git a/academic/perlprimer/doinst.sh b/academic/perlprimer/doinst.sh new file mode 100644 index 0000000000..5fb28930db --- /dev/null +++ b/academic/perlprimer/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 diff --git a/academic/perlprimer/perlprimer.SlackBuild b/academic/perlprimer/perlprimer.SlackBuild new file mode 100644 index 0000000000..87be393b78 --- /dev/null +++ b/academic/perlprimer/perlprimer.SlackBuild @@ -0,0 +1,50 @@ +#!/bin/sh + +# Slackware build script for perlprimer +# 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=perlprimer +VERSION=${VERSION:-1.1.20} +ARCH=noarch +BUILD=${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 +tar -jxvf $CWD/$PRGNAM-$VERSION.tar.bz2 +cd $PRGNAM-$VERSION + +install -D -m755 perlprimer.pl $PKG/usr/bin/perlprimer.pl + +# Menu item and icon +mkdir -p $PKG/usr/share/{applications,pixmaps} +cp $CWD/$PRGNAM.desktop $PKG/usr/share/applications/ +cp $CWD/$PRGNAM.png $PKG/usr/share/pixmaps + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + Changelog ReadMe.txt todo tutorial.html tutorial_files \ + $PKG/usr/doc/$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/perlprimer/perlprimer.desktop b/academic/perlprimer/perlprimer.desktop new file mode 100644 index 0000000000..f60fb9a287 --- /dev/null +++ b/academic/perlprimer/perlprimer.desktop @@ -0,0 +1,7 @@ +[Desktop Entry] +Categories=Education; +Exec=perlprimer.pl +Icon=perlprimer.png +Name=Perlprimer +StartupNotify=false +Type=Application diff --git a/academic/perlprimer/perlprimer.info b/academic/perlprimer/perlprimer.info new file mode 100644 index 0000000000..ad7c5f7d12 --- /dev/null +++ b/academic/perlprimer/perlprimer.info @@ -0,0 +1,10 @@ +PRGNAM="perlprimer" +VERSION="1.1.20" +HOMEPAGE="http://perlprimer.sourceforge.net/" +DOWNLOAD="http://downloads.sourceforge.net/perlprimer/perlprimer-1.1.20.tar.bz2" +MD5SUM="e3ce015cd5301aeb6120b75692008431" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +MAINTAINER="Petar Petrov" +EMAIL="ppetrov@paju.oulu.fi" +APPROVED="Niels Horn" diff --git a/academic/perlprimer/perlprimer.png b/academic/perlprimer/perlprimer.png new file mode 100644 index 0000000000..f476bbd775 Binary files /dev/null and b/academic/perlprimer/perlprimer.png differ diff --git a/academic/perlprimer/slack-desc b/academic/perlprimer/slack-desc new file mode 100644 index 0000000000..8e0df5af07 --- /dev/null +++ b/academic/perlprimer/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------------------------------------------------------| +perlprimer: perlprimer (Design primers for PCR and sequencing) +perlprimer: +perlprimer: PerlPrimer is a free, open-source GUI application written in Perl +perlprimer: that designs primers for standard PCR, bisulphite PCR, real-time PCR +perlprimer: (QPCR) and sequencing. It aims to automate and simplify the process +perlprimer: of primer design. +perlprimer: +perlprimer: +perlprimer: +perlprimer: References: /usr/doc/perlprimer-$VERSION/References +perlprimer: Home: http://perlprimer.sourceforge.net/ -- cgit v1.2.3