From 00668f37751b72fa4f3f08d2152190277f9f1f17 Mon Sep 17 00:00:00 2001 From: Petar Petrov Date: Fri, 2 Sep 2011 22:19:20 -0300 Subject: academic/primer3: Added (Design PCR primers) Signed-off-by: Niels Horn --- academic/primer3/README | 11 +++++ academic/primer3/References | 6 +++ academic/primer3/primer3.SlackBuild | 93 +++++++++++++++++++++++++++++++++++++ academic/primer3/primer3.info | 10 ++++ academic/primer3/slack-desc | 19 ++++++++ 5 files changed, 139 insertions(+) create mode 100644 academic/primer3/README create mode 100644 academic/primer3/References create mode 100644 academic/primer3/primer3.SlackBuild create mode 100644 academic/primer3/primer3.info create mode 100644 academic/primer3/slack-desc (limited to 'academic') diff --git a/academic/primer3/README b/academic/primer3/README new file mode 100644 index 0000000000..2ef54f3a5a --- /dev/null +++ b/academic/primer3/README @@ -0,0 +1,11 @@ +Primer3 is a widely used program for designing PCR primers. Primer3 +can also design hybridization probes and sequencing primers. PCR is +used for many different goals. Consequently, primer3 has many +different input parameters that you control and that tell primer3 +exactly what characteristics make good primers for your goals. + +For details and citation: +Steve Rozen and Helen J. Skaletsky (2000) Primer3 on the WWW for +general users and for biologist programmers. In: Krawetz S, Misener S +(eds) Bioinformatics Methods and Protocols: Methods in Molecular +Biology. Humana Press, Totowa, NJ, pp 365-386 diff --git a/academic/primer3/References b/academic/primer3/References new file mode 100644 index 0000000000..7f4646bd80 --- /dev/null +++ b/academic/primer3/References @@ -0,0 +1,6 @@ +References + +Steve Rozen and Helen J. Skaletsky (2000) Primer3 on the WWW for general +users and for biologist programmers. In: Krawetz S, Misener S (eds) +Bioinformatics Methods and Protocols: Methods in Molecular Biology. Humana +Press, Totowa, NJ, pp 365-386 diff --git a/academic/primer3/primer3.SlackBuild b/academic/primer3/primer3.SlackBuild new file mode 100644 index 0000000000..fbba3a73f5 --- /dev/null +++ b/academic/primer3/primer3.SlackBuild @@ -0,0 +1,93 @@ +#!/bin/sh + +# Slackware build script for primer3 +# 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=primer3 +VERSION=${VERSION:-2.2.3} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i486 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +CWD=$(pwd) +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i486" ]; then + SLKCFLAGS="-O2 -march=i486 -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 $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION +chown -R root:root . +find . \ + \( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \ + -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ + -exec chmod 644 {} \; + +cd ./src + +#Use our CFLAGS +sed -i "/^CFLAGS/s/=/+=/" Makefile + +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ + make + +# This is recommended, but the tests take a really long time. +# Be patient if you uncomment the next line. +# make test + +install -D -m755 primer3_core $PKG/usr/bin/primer3_core +install -D -m755 long_seq_tm_test $PKG/usr/bin/long_seq_tm_test +install -D -m755 ntdpal $PKG/usr/bin/ntdpal +install -D -m755 ntthal $PKG/usr/bin/ntthal +install -D -m755 oligotm $PKG/usr/bin/oligotm + +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 \ + COPYING.txt example primer3_manual.htm \ + $PKG/usr/doc/$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/primer3/primer3.info b/academic/primer3/primer3.info new file mode 100644 index 0000000000..c87f77efde --- /dev/null +++ b/academic/primer3/primer3.info @@ -0,0 +1,10 @@ +PRGNAM="primer3" +VERSION="2.2.3" +HOMEPAGE="http://primer3.sourceforge.net/" +DOWNLOAD="http://downloads.sourceforge.net/project/primer3/primer3/2.2.3/primer3-2.2.3.tar.gz" +MD5SUM="b9cdcff68637479c094844d652c03839" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +MAINTAINER="Petar Petrov" +EMAIL="ppetrov@paju.oulu.fi" +APPROVED="Niels Horn" diff --git a/academic/primer3/slack-desc b/academic/primer3/slack-desc new file mode 100644 index 0000000000..7956929b4b --- /dev/null +++ b/academic/primer3/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------------------------------------------------------| +primer3: primer3 (Design PCR primers) +primer3: +primer3: Primer3 is a widely used program for designing PCR primers (PCR = +primer3: "Polymerase Chain Reaction"). PCR is an essential and +primer3: ubiquitous tool in genetics and molecular biology. Primer3 can also +primer3: design hybridization probes and sequencing primers. +primer3: +primer3: +primer3: +primer3: +primer3: Home: http://primer3.sourceforge.net/ -- cgit v1.2.3-65-gdbad