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academic/primer3: Updated for version 2.4.0. 

Signed-off-by: David Spencer <idlemoor@slackbuilds.org>
This commit is contained in:
Petar Petrov 2018-07-08 19:42:08 +01:00 committed by David Spencer
parent 5c821121ec
commit 4ce886af27
7 changed files with 467 additions and 16 deletions
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22
academic/primer3/gcc-7.patch Normal file
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@ -0,0 +1,22 @@
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;

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academic/primer3/man1/ntdpal.1 Normal file
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'\" t
.\" Title: NTDPAL
.\" Author: [FIXME: author] [see http://docbook.sf.net/el/author]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
.\" Date: 11/30/2011
.\" Manual: Primer3 User Manuals
.\" Source: ntdpal 1.1.4
.\" Language: English
.\"
.TH "NTDPAL" "1" "11/30/2011" "ntdpal 1.1.4" "Primer3 User Manuals"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
.\" http://bugs.debian.org/507673
.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
.ie \n(.g .ds Aq \(aq
.el .ds Aq '
.\" -----------------------------------------------------------------
.\" * set default formatting
.\" -----------------------------------------------------------------
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.\" -----------------------------------------------------------------
.\" * MAIN CONTENT STARTS HERE *
.\" -----------------------------------------------------------------
.SH "NAME"
ntdpal \- Provides Primer3\*(Aqs alignment functionality
.SH "SYNOPSIS"
.HP \w'\fBntdpal\fR\ 'u
\fBntdpal\fR [\-g\ \fIgval\fR] [\-l\ \fIlval\fR] [\-m\ \fImval\fR] [\-f1,\ f2,\ f3] [\-p] [\-s] [\-e] {\fIseq1\fR} {\fIseq2\fR} {\fImode\fR}
.SH "DESCRIPTION"
.PP
Ntdpal (NucleoTide Dynamic Programming ALignment) is a stand\-alone program that provides Primer3\*(Aqs alignment functionality (local, a\&.k\&.a\&. Smith\-Waterman, global, a\&.k\&.a\&. Needleman\-Wunsch, plus "half global")\&.
.SH "OPTIONS"
.PP
\fB\-g\fR \fIgval\fR
.RS 4
\fIgval\fR
is a (positive) float (\&.01 precision) specifying penalty for creating a gap respectively (the penalties are subtracted from the output score)
.RE
.PP
\fB\-l\fR \fIval\fR
.RS 4
\fIlval\fR
is a (positive) float (\&.01 precision) specifying penalty for lengthening a gap respectively (the penalties are subtracted from the output score)
.RE
.PP
\fB\-a\fR
.RS 4
Causes the scoring matrix to be modified by dpal_set_ambiguity_codes\&.
.RE
.PP
\fB\-e\fR
.RS 4
Causes the end position of the alignment in both sequences to be printed\&. Do not confuse with the \*(Aqe\*(Aq
\fImode\fR\&.
.RE
.PP
\fB\-f1, \-f2, \-f3\fR
.RS 4
Force specific implementations\&. \-f2 forces use an implementation that might provide more informative error messages, possibly at the expense of some speed\&.
.RE
.PP
\fB\-h\fR
.RS 4
Use a different scoring matrix: G and C matches = 3, A and T = 2, and mismatches = \-0\&.5\&. (The default scoring matrix assigns 1 to a match, and \-1 to a mismatch\&.)
.RE
.PP
\fB\-p\fR
.RS 4
Causes the alignment to be displayed on stderr\&.
.RE
.PP
\fB\-s\fR
.RS 4
causes
\fIonly\fR
the score to printed\&.
.RE
.PP
\fB\-m\fR \fImval\fR
.RS 4
is the maximum allowed gap (default is 3)\&.
.RE
.PP
\fIseq1\fR and \fIseq2\fR
.RS 4
are the sequences to be aligned\&.
.RE
.PP
\fImode\fR
.RS 4
is one of
\fIg\fR,
\fIG\fR,
\fIl\fR, or
\fIL\fR
specifying a global, global end\-anchored, local, or local end\-anchored alignment respectively\&. For backward compatibility
\fIe\fR
is equivalent to
\fIG\fR\&.
.RE
.SH "REFERENCE"
.PP
Please cite Rozen, S\&., Skaletsky, H\&. "Primer3 on the WWW for general users and for biologist programmers\&." In S\&. Krawetz and S\&. Misener, eds\&. Bioinformatics Methods and Protocols in the series Methods in Molecular Biology\&. Humana Press, Totowa, NJ, 2000, pages 365\-386\&.
.SH "SEE ALSO"
.PP
\fBprimer3_core\fR(1)
\fBoligotm\fR(1)
.SH "COPYRIGHT"
.br
Copyright \(co 1996,1997,1998,1999,2000,2001,2004,2006,2007,2008 Whitehead Institute for Biomedical Research, Steve Rozen (http://jura.wi.mit.edu/rozen), Helen Skaletsky
.br
.PP
All rights reserved\&. On Debian\-based systems, please consult
/usr/share/doc/primer3/copyright
to read the licence of ntdpal\&.
.PP
This manual page was written by Charles Plessy <plessy@debian\&.org> for the
Debian(TM)
system (but may be used by others)\&. Permission is granted to copy, distribute and/or modify this document under the same terms as oligotm itself\&.
.sp

40
academic/primer3/man1/ntthal.1 Normal file
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@ -0,0 +1,40 @@
.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.43.3.
.TH NTTHAL "1" "December 2013" "2.3.6" "Primer3 User Manuals"
.SH NAME
ntthal \- Provides Primer3's alignment functionality based on nearest-neighbor thermodynamical approach
.SH DESCRIPTION
\fBntthal\fR is analogous to \fBntdpal\fR. Between two sequences, \fBntthal\fR finds
alignment/sec structure, that has the highest melting
temperature. Ntthal is based on nearest-neighbor thermodynamical
approach.
.SH SYNOPSIS
.B ntthal
\fIOPTIONS\fR oligo
.SH OPTIONS
\fB\-mv\fR monovalent_conc \- concentration of monovalent cations in mM, by default 50 mM
.PP
\fB\-dv\fR divalent_conc \- concentration of divalent cations in mM, by default 0 mM
.PP
\fB\-n\fR dNTP_conc \- concentration of deoxynycleotide triphosphate in mM, by default 0 mM
.PP
\fB\-d\fR dna_conc \- concentration of DNA strands in nM, by default 50 nM
.PP
\fB\-a\fR mode \- alignment type, END1, END2, ANY and HAIRPIN, by default ANY (when duplex)
.PP
\fB\-t\fR temp \- temperature at which duplex is calculated, by default 37C
.PP
\fB\-r\fR \- causes the alignment NOT to be displayed on stderr, _only_ Tm is printed
.PP
\fB\-maxloop\fR size \- the maximum size of secondary structures loops.
.IP
Default is 30 (this is maximum allowed length, currently).
.PP
\fB\-path\fR <path> \- the path to the thermodynamic parameter files
.PP
\fB\-s1\fR DNA_oligomer
.PP
\fB\-s2\fR DNA_oligomer
.SH AUTHORS
This manual page was created by Andreas Tille <tille@debian.org> using help2man
for Debian but can be freely used for any other purpose

165
academic/primer3/man1/oligotm.1 Normal file
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@ -0,0 +1,165 @@
'\" t
.\" Title: OLIGOTM
.\" Author: [FIXME: author] [see http://docbook.sf.net/el/author]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
.\" Date: 11/30/2011
.\" Manual: Primer3 User Manuals
.\" Source: oligotm 1.1.4
.\" Language: English
.\"
.TH "OLIGOTM" "1" "11/30/2011" "oligotm 1.1.4" "Primer3 User Manuals"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
.\" http://bugs.debian.org/507673
.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
.ie \n(.g .ds Aq \(aq
.el .ds Aq '
.\" -----------------------------------------------------------------
.\" * set default formatting
.\" -----------------------------------------------------------------
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.\" -----------------------------------------------------------------
.\" * MAIN CONTENT STARTS HERE *
.\" -----------------------------------------------------------------
.SH "NAME"
oligotm \- Prints oligo\*(Aqs melting temperature on stdout
.SH "SYNOPSIS"
.HP \w'\fBoligotm\fR\ 'u
\fBoligotm\fR [OPTIONS] {oligo}
.PP
where oligo is a DNA sequence of between 2 and 36 bases
.SH "DESCRIPTION"
.PP
\fBoligotm\fR
prints the melting temperature of a given deoxyribonucleotide on the standard output\&. It is part of the oligotm library\&.
.SH "OPTIONS"
.PP
\fB\-mv\fR \fImonovalent_conc\fR
.RS 4
Concentration of monovalent cations in mM, by default 50\ \&mM\&.
.RE
.PP
\fB\-dv\fR \fIdivalent_conc\fR
.RS 4
Concentration of divalent cations in mM, by default 0\ \&mM\&.
.RE
.PP
\fB\-n\fR \fIdNTP_conc\fR
.RS 4
Concentration of deoxynucleotide triphosphate in mM, by default 0\ \&mM\&.
.RE
.PP
\fB\-d\fR \fIdna_conc\fR
.RS 4
Concentration of DNA strands in nM, by default 50\ \&nM\&.
.RE
.PP
\fB\-tp\fR \fI[0|1]\fR
.RS 4
Specifies the table of thermodynamic parameters and the method of melting temperature calculation:
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.sp -1
.IP \(bu 2.3
.\}
\fI0\fR
Breslauer et al\&., 1986 and Rychlik et al\&., 1990 (used by primer3 up to and including release 1\&.1\&.0)\&. This is the default, but
\fInot\fR
the recommended value\&.
.RE
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.sp -1
.IP \(bu 2.3
.\}
\fI1\fR
Use nearest neighbor parameter from SantaLucia 1998\&.
\fIThis is the recommended value\fR\&.
.RE
.RE
.PP
\fB\-sc\fR \fI[0\&.\&.2]\fR
.RS 4
Specifies salt correction formula for the melting temperature calculation:
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.sp -1
.IP \(bu 2.3
.\}
\fI0\fR
Schildkraut and Lifson 1965, used by primer3 up to and including release 1\&.1\&.0\&. This is the default, but
\fInot\fR
the recommended value\&.
.RE
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.sp -1
.IP \(bu 2.3
.\}
\fI1\fR
SantaLucia 1998\&.
\fIThis is the recommended value\fR\&.
.RE
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.sp -1
.IP \(bu 2.3
.\}
\fI2\fR
Owczarzy et al\&., 2004\&.
.RE
.RE
.PP
\fB\-i\fR
.RS 4
prints references to publications which were used for thermodynamic calculations\&.
.RE
.SH "REFERENCE"
.PP
Please cite Rozen, S\&., Skaletsky, H\&. "Primer3 on the WWW for general users and for biologist programmers\&." In S\&. Krawetz and S\&. Misener, eds\&. Bioinformatics Methods and Protocols in the series Methods in Molecular Biology\&. Humana Press, Totowa, NJ, 2000, pages 365\-386\&.
.SH "SEE ALSO"
.PP
\fBprimer3_core\fR(1)
\fBntdpal\fR(1)
.SH "COPYRIGHT"
.br
Copyright \(co 1996,1997,1998,1999,2000,2001,2004,2006,2007,2008 Whitehead Institute for Biomedical Research, Steve Rozen (http://jura.wi.mit.edu/rozen), Helen Skaletsky
.br
.PP
All rights reserved\&. On Debian\-based systems, please consult
/usr/share/doc/primer3/copyright
to read the licence of oligotm\&.
.PP
This manual page was written by Charles Plessy <plessy@debian\&.org> for the
Debian(TM)
system (but may be used by others)\&. Permission is granted to copy, distribute and/or modify this document under the same terms as oligotm itself\&.
.sp

90
academic/primer3/man1/primer3_core.1 Normal file
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@ -0,0 +1,90 @@
.\" Title: PRIMER3_CORE
.\" Author:
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
.\" Date: 05/09/2008
.\" Manual: Primer3 User Manuals
.\" Source: primer3_core 1.1.4
.\"
.TH "PRIMER3_CORE" "1" "05/09/2008" "primer3_core 1.1.4" "Primer3 User Manuals"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
primer3_core \- Designs primers for PCR
.SH "SYNOPSIS"
.HP 13
\fBprimer3_core\fR [\-format_output] [\-strict_tags] [<\ \fIinput_file\fR]
.SH "DESCRIPTION"
.PP
primer3_core 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 sequence, and miscellaneous other constraints\&.
.PP
By default, primer3_core accepts input and produces output in Boulder\-io format, a pre\-XML text\-based input/output format for program\-to\-program data interchange format\&. The Boulder\-io format and the commands that primer3_core understands are described in the
\fIREADME\fR
file, which on Debian systems can be found in
\fI/usr/share/doc/primer3/\fR\&.
.SH "OPTIONS"
.PP
\fB\-format_output\fR
.RS 4
Prints a more user\-oriented report for each sequence\&.
.RE
.PP
\fB\-strict_tags\fR
.RS 4
primer3_core echoes and ignores any tags it does not recognize, unless the
\fB\-strict_tags\fR
flag is set on the command line, in which case primer3_core prints an error in the PRIMER_ERROR output tag, and prints additional information on stdout; this option can be useful for debugging systems that incorporate primer\&.
.RE
.sp
.it 1 an-trap
.nr an-no-space-flag 1
.nr an-break-flag 1
.br
Note
.PP
The old flag \-2x_compat is no longer supported\&.
.SH "EXIT STATUS CODES"
.sp
.RS 4
\h'-04'\(bu\h'+03'0 on normal operation\&.
.RE
.sp
.RS 4
\h'-04'\(bu\h'+03'\-1 under the following conditions: illegal command\-line arguments, unable to fflush stdout, unable to open (for writing and creating) a \&.for, \&.rev or \&.int file (probably due to a protection problem)\&.
.RE
.sp
.RS 4
\h'-04'\(bu\h'+03'\-2 on out\-of\-memory\&.
.RE
.sp
.RS 4
\h'-04'\(bu\h'+03'\-3 empty input\&.
.RE
.sp
.RS 4
\h'-04'\(bu\h'+03'\-4 error in a "Global" input tag (message in PRIMER_ERROR)\&.
.RE
.SH "REFERENCE"
.PP
Please cite Rozen, S\&., Skaletsky, H\&. "Primer3 on the WWW for general users and for biologist programmers\&." In S\&. Krawetz and S\&. Misener, eds\&. Bioinformatics Methods and Protocols in the series Methods in Molecular Biology\&. Humana Press, Totowa, NJ, 2000, pages 365\-386\&.
.SH "SEE ALSO"
.PP
\fBntdpal\fR(1)
\fBoligotm\fR(1)
.SH "COPYRIGHT"
Copyright \(co 1996,1997,1998,1999,2000,2001,2004,2006,2007,2008 Whitehead Institute for Biomedical Research, Steve Rozen (http://jura.wi.mit.edu/rozen), Helen Skaletsky
.br
.PP
All rights reserved\&. On Debian\-based systems, please consult
\fI/usr/share/doc/primer3/copyright\fR
to read the licence of primer3_core\&.
.PP
This manual page was written by Steffen Moeller
<moeller@debian\&.org>
for the
Debian(TM)
system (but may be used by others)\&. Permission is granted to copy, distribute and/or modify this document under the same terms as primer3_core itself\&.
.sp

32
academic/primer3/primer3.SlackBuild
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@ -2,7 +2,7 @@
# Slackware build script for primer3
# Copyright 2011-2016 Petar Petrov slackalaxy@gmail.com
# Copyright 2011-2018 Petar Petrov slackalaxy@gmail.com
# All rights reserved.
#
# Redistribution and use of this script, with or without modification, is
@ -23,13 +23,13 @@
# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
PRGNAM=primer3
VERSION=${VERSION:-2.3.7}
VERSION=${VERSION:-2.4.0}
BUILD=${BUILD:-1}
TAG=${TAG:-_SBo}
if [ -z "$ARCH" ]; then
case "$( uname -m )" in
i?86) ARCH=i486 ;;
i?86) ARCH=i586 ;;
arm*) ARCH=arm ;;
*) ARCH=$( uname -m ) ;;
esac
@ -40,8 +40,8 @@ TMP=${TMP:-/tmp/SBo}
PKG=$TMP/package-$PRGNAM
OUTPUT=${OUTPUT:-/tmp}
if [ "$ARCH" = "i486" ]; then
SLKCFLAGS="-O2 -march=i486 -mtune=i686"
if [ "$ARCH" = "i586" ]; then
SLKCFLAGS="-O2 -march=i586 -mtune=i686"
LIBDIRSUFFIX=""
elif [ "$ARCH" = "i686" ]; then
SLKCFLAGS="-O2 -march=i686 -mtune=i686"
@ -69,6 +69,9 @@ 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 $CWD/gcc-7.patch
cd ./src
# Use our CFLAGS
@ -81,8 +84,8 @@ CFLAGS="$SLKCFLAGS" \
CXXFLAGS="$SLKCFLAGS" \
make
# This is recommended, but the tests take a really long time.
# Be patient if you uncomment the next line.
# This is recommended, but the tests take a really long time. Be patient
# if you uncomment the line below.
# make test
install -D -m755 primer3_core $PKG/usr/bin/primer3_core
@ -97,18 +100,21 @@ 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
cp -a settings_files src/primer3_config $PKG/usr/share/$PRGNAM
# Copy the man pages from Debian
mkdir -p $PKG/usr/man/man1
cp $CWD/man1/* $PKG/usr/man/man1
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
find $PKG/usr/man -type f -exec gzip -9 {} \;
for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done
mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
cp -a \
src/release_notes.txt COPYING.txt example primer3_manual.htm \
src/{release_notes.txt,primer3_manual.htm} LICENSE example 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

6
academic/primer3/primer3.info
View File

@ -1,8 +1,8 @@
PRGNAM="primer3"
VERSION="2.3.7"
VERSION="2.4.0"
HOMEPAGE="http://primer3.sourceforge.net/"
DOWNLOAD="http://sourceforge.net/projects/primer3/files/primer3/2.3.7/primer3-2.3.7.tar.gz"
MD5SUM="c6b89067bf465e62b6b1fd830b5b4418"
DOWNLOAD="http://sourceforge.net/projects/primer3/files/primer3/2.4.0/primer3-2.4.0.tar.gz"
MD5SUM="aed6546bdfb60652cd7eba8d51eae8cc"
DOWNLOAD_x86_64=""
MD5SUM_x86_64=""
REQUIRES=""