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academic/primer3: Updated for version 2.6.1.

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Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>
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Petar Petrov 2023-06-20 19:52:13 +07:00 committed by Willy Sudiarto Raharjo
parent 7186da9e9e
commit 3675807988
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6 changed files with 53 additions and 52 deletions
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26
academic/primer3/README
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@ -1,14 +1,24 @@
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.
"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
Biology. Humana Press, Totowa, NJ, pp 365-386
Primer3 picks primers for PCR reactions, considering as criteria:
* oligonucleotide melting temperature, size, GC content and primer-dimer
possibilities,
* PCR product size
* positional constraints within the source (template) sequence
* possibilities for ectopic priming (amplifying the wrong sequence)
* many other constraints.
All of these criteria are user-specifiable as constraints, and some are
specifiable as terms in an objective function that characterizes an
optimal primer pair.
manual online: https://primer3.org/manual.html
For details and citation see "References" in the package's doc folder.

25
academic/primer3/References
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@ -1,4 +1,21 @@
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
We request but do not require that use of this software be cited in publications as
* Untergasser A, Cutcutache I, Koressaar T, Ye J, Faircloth BC, Remm M and Rozen SG.
Primer3--new capabilities and interfaces.
Nucleic Acids Res. 2012 Aug 1;40(15):e115.
The paper is available at http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3424584/
and
* Koressaar T and Remm M.
Enhancements and modifications of primer design program Primer3.
Bioinformatics 2007;23(10):1289-1291.
The paper is available at https://www.ncbi.nlm.nih.gov/pubmed/17379693
If you use masker function, please cite:
* Koressaar T, Lepamets M, Kaplinski L, Raime K, Andreson R and Remm M.
Primer3_masker: integrating masking of template sequence with primer design software.
Bioinformatics 2018;34(11):1937-1938.
The paper is available at https://www.ncbi.nlm.nih.gov/pubmed/29360956
Source code available at https://github.com/primer3-org/primer3.

22
academic/primer3/gcc-7.patch
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@ -1,22 +0,0 @@
Author: Andreas Tille <tille@debian.org>
Last-Update: Sat, 26 Aug 2017 00:32:40 +0200
Bug-Debian: https://bugs.debian.org/853621
Description: Fix build with gcc-7
--- a/src/thal.c
+++ b/src/thal.c
@@ -426,12 +426,12 @@ thal(const unsigned char *oligo_f,
"Illegal type");
o->align_end_1 = -1;
o->align_end_2 = -1;
- if ('\0' == oligo_f) {
+ if ('\0' == oligo_f[0]) {
strcpy(o->msg, "Empty first sequence");
o->temp = 0.0;
return;
}
- if ('\0' == oligo_r) {
+ if ('\0' == oligo_r[0]) {
strcpy(o->msg, "Empty second sequence");
o->temp = 0.0;
return;

20
academic/primer3/primer3.SlackBuild
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@ -2,7 +2,7 @@
# Slackware build script for primer3
# Copyright 2011-2021 Petar Petrov slackalaxy@gmail.com
# Copyright 2011-2023 Petar Petrov slackalaxy@gmail.com
# All rights reserved.
#
# Redistribution and use of this script, with or without modification, is
@ -25,7 +25,7 @@
cd $(dirname $0) ; CWD=$(pwd)
PRGNAM=primer3
VERSION=${VERSION:-2.4.0}
VERSION=${VERSION:-2.6.1}
BUILD=${BUILD:-1}
TAG=${TAG:-_SBo}
PKGTYPE=${PKGTYPE:-tgz}
@ -38,9 +38,6 @@ if [ -z "$ARCH" ]; then
esac
fi
# If the variable PRINT_PACKAGE_NAME is set, then this script will report what
# the name of the created package would be, and then exit. This information
# could be useful to other scripts.
if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then
echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE"
exit 0
@ -79,13 +76,10 @@ find -L . \
\( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \
-o -perm 440 -o -perm 400 \) -exec chmod 644 {} \;
# Thanks to Debian for the patch
patch -p1 -i $CWD/gcc-7.patch
cd ./src
# Use our CFLAGS
sed -i -e "s|-O2|$SLKCFLAGS|" -e "s|-g -Wall|-fpermissive|" Makefile
sed -i -e "s|-O2|$SLKCFLAGS|" Makefile
# Look for configuration files in /usr/share instead of /opt
sed -i "s:/opt/primer3_config:/usr/share/$PRGNAM/primer3_config:g" thal_main.c primer3_boulder_main.c
@ -94,7 +88,7 @@ make
# This is recommended, but the tests take a really long time. Be patient
# if you uncomment the line below.
# make test
#make test
install -D -m755 primer3_core $PKG/usr/bin/primer3_core
install -D -m755 ntdpal $PKG/usr/bin/ntdpal
@ -108,7 +102,9 @@ 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 settings_files src/primer3_config $PKG/usr/share/$PRGNAM
cp -a \
kmer_lists/readme.txt settings_files example src/primer3_config \
$PKG/usr/share/$PRGNAM
# Copy the man pages from Debian
mkdir -p $PKG/usr/man/man1
@ -122,7 +118,7 @@ for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; r
mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
cp -a \
src/{release_notes.txt,primer3_manual.htm} LICENSE example README.md \
src/{release_notes.txt,primer3_manual.htm} LICENSE README.md \
$PKG/usr/doc/$PRGNAM-$VERSION
cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References

8
academic/primer3/primer3.info
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@ -1,8 +1,8 @@
PRGNAM="primer3"
VERSION="2.4.0"
HOMEPAGE="http://primer3.sourceforge.net/"
DOWNLOAD="http://sourceforge.net/projects/primer3/files/primer3/2.4.0/primer3-2.4.0.tar.gz"
MD5SUM="aed6546bdfb60652cd7eba8d51eae8cc"
VERSION="2.6.1"
HOMEPAGE="https://primer3.org/"
DOWNLOAD="https://github.com/primer3-org/primer3/archive/v2.6.1/primer3-2.6.1.tar.gz"
MD5SUM="d18c095694b586c300c88fab4b116c8c"
DOWNLOAD_x86_64=""
MD5SUM_x86_64=""
REQUIRES=""

4
academic/primer3/slack-desc
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@ -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: References: /usr/doc/primer3-2.3.7/References
primer3: https://primer3.org/manual.html
primer3:
primer3:
primer3: