diff options
Diffstat (limited to 'academic/primer3')
| -rw-r--r-- | academic/primer3/README | 17 | ||||
| -rw-r--r-- | academic/primer3/References | 2 | ||||
| -rw-r--r-- | academic/primer3/primer3.SlackBuild | 47 | ||||
| -rw-r--r-- | academic/primer3/primer3.info | 6 | ||||
| -rw-r--r-- | academic/primer3/slack-desc | 2 |
5 files changed, 49 insertions, 25 deletions
diff --git a/academic/primer3/README b/academic/primer3/README index 2ef54f3a5a6eb..51977f2f124c8 100644 --- a/academic/primer3/README +++ b/academic/primer3/README @@ -1,11 +1,14 @@ -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 +Primer3 is a widely used program for designing PCR primers (PCR = +"Polymerase Chain Reaction"). PCR is an essential and ubiquitous tool +in genetics and molecular biology. Primer3 can 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 +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 index 7f4646bd80580..5009a52a1bc33 100644 --- a/academic/primer3/References +++ b/academic/primer3/References @@ -1,5 +1,3 @@ -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 diff --git a/academic/primer3/primer3.SlackBuild b/academic/primer3/primer3.SlackBuild index 150008b4f3194..09cf5104ce09d 100644 --- a/academic/primer3/primer3.SlackBuild +++ b/academic/primer3/primer3.SlackBuild @@ -1,18 +1,30 @@ #!/bin/sh # Slackware build script for primer3 -# Written by Petar Petrov, <ppetrov@paju.oulu.fi> and -# hereby submitted to the public domain -# Thanks to Niels Horn for correcting the CFLAGS. - -# 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. +# Copyright 2011-2012 Petar Petrov, ppetrov@paju.oulu.fi +# 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=primer3 -VERSION=${VERSION:-2.2.3} -BUILD=${BUILD:-2} +VERSION=${VERSION:-2.3.4} +BUILD=${BUILD:-1} TAG=${TAG:-_SBo} if [ -z "$ARCH" ]; then @@ -62,6 +74,9 @@ cd ./src #Use our CFLAGS sed -i "/^CFLAGS/s/=/+=/" Makefile +# Look for configuration files in /usr/share instead of /opt +sed -i "s:/opt/primer3_config:/usr/share/$PRGNAM/primer3_config:g" thal_main.c primer3_boulder_main.c + CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS" \ make @@ -71,14 +86,22 @@ make # 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 -# eprimer32 from EMBOSS expects the binary to be called primer32_core -ln -s primer3_core $PKG/usr/bin/primer32_core +# eprimer32 from EMBOSS, expects the binary to be called primer32_core +cd $PKG/usr/bin +ln -s primer3_core primer32_core + +# Copy configuration files and settings to /usr/share cd $TMP/$PRGNAM-$VERSION +mkdir -p $PKG/usr/share/$PRGNAM +cp -a src/primer3_config \ + primer3_v1_1_4_default_settings.txt \ + primer3web_v0_4_0_default_settings.txt \ + primer3web_v3_0_0_default_settings.txt \ + $PKG/usr/share/$PRGNAM 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 diff --git a/academic/primer3/primer3.info b/academic/primer3/primer3.info index 3ebd4bbaa2842..9c5bb8fbb98b0 100644 --- a/academic/primer3/primer3.info +++ b/academic/primer3/primer3.info @@ -1,8 +1,8 @@ PRGNAM="primer3" -VERSION="2.2.3" +VERSION="2.3.4" 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="http://downloads.sourceforge.net/project/primer3/primer3/2.3.4/primer3-2.3.4.tar.gz" +MD5SUM="06029a16dccf1bcec70fd427d3c44850" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" diff --git a/academic/primer3/slack-desc b/academic/primer3/slack-desc index 7956929b4b24e..dae2bbb6a5f0b 100644 --- a/academic/primer3/slack-desc +++ b/academic/primer3/slack-desc @@ -13,7 +13,7 @@ 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: Home: http://primer3.sourceforge.net/ primer3: primer3: primer3: -primer3: Home: http://primer3.sourceforge.net/ |