debian/0000755000000000000000000000000012254547623007200 5ustar debian/control0000644000000000000000000000224012254540352010571 0ustar Source: primer3 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Charles Plessy , Andreas Tille Section: science Priority: optional Build-Depends: debhelper (>= 9) Standards-Version: 3.9.5 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/primer3/trunk/ Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/primer3/trunk/ Homepage: http://primer3.sourceforge.net Package: primer3 Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Suggests: ncbi-epcr Enhances: emboss Description: Tool to design flanking oligo nucleotides for DNA amplification Primer3 picks primers for Polymerase Chain Reactions (PCRs), 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. 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. debian/oligotm.10000644000000000000000000001032312214301054010711 0ustar '\" t .\" Title: OLIGOTM .\" Author: [FIXME: author] [see http://docbook.sf.net/el/author] .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" 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 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 debian/rules0000755000000000000000000000016212254532757010261 0ustar #!/usr/bin/make -f %: dh $@ --sourcedirectory=src override_dh_auto_test: dh_auto_test --sourcedirectory=test debian/primer3.examples0000644000000000000000000000001012214301054012266 0ustar example debian/watch0000644000000000000000000000014112254532450010215 0ustar version=3 http://sf.net/primer3/primer3-[-src]*([\d.]*)\.(?:tgz|tbz|txz|(?:tar\.(?:gz|bz2|xz))) debian/upstream0000644000000000000000000000144712214301054010747 0ustar Contact: Steve Rozen (http://purl.com/STEVEROZEN/) Homepage: http://primer3.sourceforge.net Name: Primer3 Reference: Author: Steve Rozen and Helen J. Skaletsky Year: 2000 Title: Primer3 on the WWW for general users and for biologist programmers Booktitle: > Bioinformatics Methods and Protocols: Methods in Molecular Biology Journal: Methods Mol Biol. Pages: 365-86 Volume: 132 Number: 3 Publisher: Humana Press Editor: Krawetz S, Misener S PMID: 10547847 DOI: 10.1385/1-59259-192-2:365 URL: http://www.springerlink.com/content/u16755q84278vh5w/ eprint: http://www.springerlink.com/content/u16755q84278vh5w/fulltext.pdf Watch: http://sf.net/primer3/primer3-([\d.]*)\.tar\.gz Webservice: - http://frodo.wi.mit.edu/primer3/ - http://www.bioinformatics.nl/cgi-bin/primer3plus/primer3plus.cgi debian/copyright0000644000000000000000000000455512232766653011146 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Source: http://qa.debian.org/watch/sf.php/primer3/primer3-2.3.6.tar.gz Files: * Copyright: © 1996,1997,1998,1999,2000,2001,2004,2006,2007,2008,2009,2010,2011,2012 Whitehead Institute for Biomedical Research, Steve Rozen (http://purl.com/STEVEROZEN/), Andreas Untergasser and Helen Skaletsky All rights reserved. License: GPL-2+ Files: debian/* Copyright: © 2004 Steffen Möller © 2006-2008 Charles Plessy © 2008 David Paleino © 2012-2013 Andreas Tille License: GPL-2+ License: GPL-2+ This file is part of the primer3 suite and libraries. . The primer3 suite and libraries are free software; you can redistribute them and/or modify them under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. . This software is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. . You should have received a copy of the GNU General Public License along with this software (file gpl-2.0.txt in the source distribution); if not, write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA . THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "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 COPYRIGHT OWNERS OR CONTRIBUTORS 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. Comment: On Debian systems, the complete text of the GNU General Public License version 2 can be found in `/usr/share/common-licenses/GPL-2'. debian/primer3.doc-base0000644000000000000000000000122412214301054012135 0ustar Document: primer3-manual Title: Primer3 release 2.2.3 manual Author: Steve Rozen and Helen Skaletsky Abstract: Tool to design flanking oligo nucleotides for DNA amplification 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, and * possibilities for ectopic priming (amplifying the wrong sequence) * many other constraints. Section: Science/Biology Format: html Index: /usr/share/doc/primer3/primer3_manual.htm Files: /usr/share/doc/primer3/primer3_manual.htm debian/primer3.manpages0000644000000000000000000000001312254547055012267 0ustar debian/*.1 debian/ntthal.10000644000000000000000000000315512254546562010561 0ustar .\" 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 \- 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 using help2man for Debian but can be freely used for any other purpose debian/source/0000755000000000000000000000000012214301054010456 5ustar debian/source/format0000644000000000000000000000001412214301054011664 0ustar 3.0 (quilt) debian/README.test0000644000000000000000000000046212214301054011016 0ustar Primer3 for Debian ------------------ The tests included in the sources of Primer3 are ran during the building process. You can check the logs at the following address: http://buildd.debian.org/build.cgi?pkg=primer3 -- Charles Plessy Tue, 12 Feb 2008 23:22:04 +0900 debian/primer3.docs0000644000000000000000000000007412214301054011412 0ustar primer3_manual.htm src/release_notes.txt debian/README.test debian/changelog0000644000000000000000000001360312254547623011055 0ustar primer3 (2.3.6-1) unstable; urgency=low [ Charles Plessy ] * New upstream release. * Install configuration files in /etc (first step to fix bug 702693). * Normalised debian/control with config-model-edit. * Use canonical VCS URLs. [ Andreas Tille ] * Fix watch file * replace cdbs by dh * debian/patches/hardening.patch: Propagate hardening options * Standards-Version: 3.9.5 (no changes needed) * debian/patches/primer_thermodynamic_parameters_path_2_etc.patch: Make sure config files will be searched for in /etc/primer3_config/ instead of /opt/primer3_config/ Closes: #702693 * Verified that new upstream Closes: #716151, #716213 * New executable: ntthal (including manpage) * Removed *.xml variants of manpages to reduce redundancy -- Andreas Tille Thu, 19 Dec 2013 09:58:19 +0100 primer3 (2.3.5-1) unstable; urgency=low New upstream release. [ Andreas Tille ] * debian/upstream: - Remove duplicated entry for PMID - Added Volume, fixed Number - Added URL+eprint * debian/control: - Removed DM-Upload-Allowed - Standards-Version: 3.9.4 (no changes needed) * debhelper 9 (control+compat) * debian/copyright: PD License should be avoided - bumped packaging to same license as program itself -- Andreas Tille Tue, 05 Feb 2013 10:11:37 +0100 primer3 (2.3.2-1) unstable; urgency=low * New upstream release changing some default values. * Refreshed debian/copyright to machine-readable format version 1.0. Note that the license of Primer3 version 2.x changed to the GPLv2 or higher. * Spellchecked manual pages (Closes: #650477, thanks to A. Costa). * Using Debhelper 8 (debian/control, debian/compat). * Renamed debian/README.Debian debian/README.test as it is all about tests. * Conforms to Policy 3.9.3 (debian/control, no other changes needed). -- Charles Plessy Thu, 22 Mar 2012 13:35:35 +0900 primer3 (2.2.3-1) unstable; urgency=low * New upstream version * debian/primer3.docs: s/README.txt/primer3_manual.htm/ * debian/compat: 7 * debian/control: - Build-Depends: debhelper (>= 7) - Standards-Version: 3.9.1 (no changes needed * debian/source/format: 3.0 (quilt) * debian/README.source * debian/primer3.doc-base -- Andreas Tille Wed, 17 Nov 2010 14:01:59 +0100 primer3 (1.1.4-2) UNRELEASED; urgency=low [ David Paleino ] * Removed myself from Uploaders [ Charles Plessy ] * Documented informations in ‘debian/upstream-metadata.yaml’. * Removed mention of the bibliographic reference and the webservice in ‘debian/control’. -- David Paleino Sat, 23 May 2009 14:47:37 +0200 primer3 (1.1.4-1) unstable; urgency=low * New upstream release (No changes on Linux systems). * Updated my email address (debian/control, debian/copyright, manpages). * Updated the manpages: - using DocBook 4.5 - incremented Primer3 version to 1.1.4 -- Charles Plessy Fri, 09 May 2008 12:54:28 +0900 primer3 (1.1.3-1) unstable; urgency=low [ Charles Plessy ] * New upstream version: - 1.1.3: Corrected static buffer overflow errors in boulder_print_pairs() and boulder_print_oligos() in primer3_main.c. - 1.1.2: Updates to dpal.c so that no error forces an exit. Adpatation in primer3_main.c and ntdpal_main.c to updated error handling in dpal(). Arranged for primer3_main.c align() to check for and circumvent local alignments to "targets" < 3 nucleotides long, and added tests for this condition. Comment and code readability updates in dpal.h and dpal.c * Moved the Homepage: field out from the package's description. * debian/control: updated Steffen's email address. * debian/*.1.xml: corrected the headers of the sources of manpages. * debian/rules: converted to CDBS. [ David Paleino ] * debian/ntdpal.1, debian/primer3_core.1 and debian/oligotm.1 added - manpages are statically built now * debian/control: - B-D updated - added myself to Uploaders * Updated to Standards-Version 3.7.3 (no changes needed) -- Charles Plessy Mon, 25 Feb 2008 16:31:58 +0900 primer3 (1.1.1-1) unstable; urgency=low * New upstream release. * Enhances: emboss because EMBOSS has a wrapper for primer3_core. * Add Subversion repository URL to debian/control. * Updated the manpages -- Charles Plessy Sun, 3 Jun 2007 16:16:19 +0900 primer3 (1.1.0~beta-1) experimental; urgency=low * New upstream release. - Some part of primer3 is now licenced under the GNU GPL. - The oligtotm() function is now provided as a library, liboligotm. - The oligotm executable now takes additional arguments. - Non-backward compatible change: removed support of flag -2x_compat. * Added a watch file now that the sources are hosted on SourceForge.net. * Updated manpages. -- Charles Plessy Sun, 18 Feb 2007 09:04:16 +0900 primer3 (1.0b-1) unstable; urgency=low * Initial release. (Closes: #241235) * New upstream version released under a revised BSD licence. * Swiching to collaborative maintainance: Maintainer is a mailing-list, Uploaders are real people. * Using debhelper v5 and conforming to policy 3.7.2. * Relicencing the manpage of Primer3 (thanks to Steffen Moeller), adding one for ntdpal and oligotm. * Extensive tests during bulding, except on slow architectures. -- Charles Plessy Thu, 28 Sep 2006 20:18:54 +0900 primer3 (0.9-0.2) unstable; urgency=low * Contacted upstream author, change of section to non-free/optional. -- Steffen Moeller Wed, 1 Apr 2004 15:07:10 +0200 primer3 (0.9-0.1) unstable; urgency=low * Pre-Release. -- Steffen Moeller Wed, 31 Mar 2004 15:07:10 +0200 debian/primer3_core.10000644000000000000000000000626712214301054011644 0ustar .\" Title: PRIMER3_CORE .\" Author: .\" Generator: DocBook XSL Stylesheets v1.73.2 .\" 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 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 debian/patches/0000755000000000000000000000000012254541736010626 5ustar debian/patches/hardening.patch0000644000000000000000000000157712254537336013621 0ustar Author: Andreas Tille Last-Update: Thu, 19 Dec 2013 09:58:19 +0100 Description: Propagate hardening options --- a/src/Makefile +++ b/src/Makefile @@ -59,8 +59,8 @@ O_OPTS = -O2 CC_OPTS = -g -Wall -D__USE_FIXED_PROTOTYPES__ P_DEFINES = -CFLAGS = $(CC_OPTS) $(O_OPTS) -LDFLAGS = -g +CFLAGS += $(CC_OPTS) $(O_OPTS) +LDFLAGS += -g # Note, for profiling, use # make O_OPTS='-pg -O0' LDFLAGS='-g -pg' @@ -163,7 +163,7 @@ $(NTTHAL_EXE): thal_main.o thal.o $(CPP) $(LDFLAGS) -o $@ thal_main.o thal.o $(LDLIBS) $(OLIGOTM_EXE): oligotm_main.c oligotm.h $(LIBOLIGOTM) - $(CPP) $(CFLAGS) -o $@ oligotm_main.c $(LIBOLIGOTM) $(LIBOPTS) $(LDLIBS) + $(CPP) $(CFLAGS) $(LDFLAGS) -o $@ oligotm_main.c $(LIBOLIGOTM) $(LIBOPTS) $(LDLIBS) $(LONG_SEQ_EXE): long_seq_tm_test_main.c oligotm.o $(CPP) $(CFLAGS) -o $@ long_seq_tm_test_main.c oligotm.o $(LIBOPTS) $(LDLIBS) debian/patches/series0000644000000000000000000000010112254540727012032 0ustar hardening.patch primer_thermodynamic_parameters_path_2_etc.patch debian/patches/primer_thermodynamic_parameters_path_2_etc.patch0000644000000000000000000001065312254541736022410 0ustar Author: Andreas Tille Last-Changed: Thu, 19 Dec 2013 09:58:19 +0100 Bug-Debian: http://bugs.debian.org/702693 Description: Configuration in /etc Make sure config files will be searched for in /etc/primer3_config/ instead of /opt/primer3_config/ --- a/src/primer3_boulder_main.c +++ b/src/primer3_boulder_main.c @@ -505,18 +505,18 @@ read_thermodynamic_parameters() return; } #else - /* in linux, check for ./primer3_config and /opt/primer3_config */ + /* in Debian, check for ./primer3_config and /etc/primer3_config */ struct stat st; if ((stat("./primer3_config", &st) == 0) && S_ISDIR(st.st_mode)) { thermodynamic_params_path = (char*) malloc(strlen("./primer3_config/") * sizeof(char) + 1); if (NULL == thermodynamic_params_path) exit (-2); /* Out of memory */ strcpy(thermodynamic_params_path, "./primer3_config/"); - } else if ((stat("/opt/primer3_config", &st) == 0) && S_ISDIR(st.st_mode)) { + } else if ((stat("/etc/primer3_config", &st) == 0) && S_ISDIR(st.st_mode)) { thermodynamic_params_path = - (char*) malloc(strlen("/opt/primer3_config/") * sizeof(char) + 1); + (char*) malloc(strlen("/etc/primer3_config/") * sizeof(char) + 1); if (NULL == thermodynamic_params_path) exit (-2); /* Out of memory */ - strcpy(thermodynamic_params_path, "/opt/primer3_config/"); + strcpy(thermodynamic_params_path, "/etc/primer3_config/"); } else { /* no default directory found */ return; --- a/src/thal_main.c +++ b/src/thal_main.c @@ -303,8 +303,8 @@ if(a.debug == 0) { #else if ((stat("./primer3_config", &st) == 0) && S_ISDIR(st.st_mode)) { tmp_ret = get_thermodynamic_values("./primer3_config/", &o); - } else if ((stat("/opt/primer3_config", &st) == 0) && S_ISDIR(st.st_mode)) { - tmp_ret = get_thermodynamic_values("/opt/primer3_config/", &o); + } else if ((stat("/etc/primer3_config", &st) == 0) && S_ISDIR(st.st_mode)) { + tmp_ret = get_thermodynamic_values("/etc/primer3_config/", &o); } else { /* no default directory found, error */ fprintf(stderr, "Error: thermodynamic approach chosen, but path to thermodynamic parameters not specified\n"); --- a/src/release_notes.txt +++ b/src/release_notes.txt @@ -151,9 +151,9 @@ defaults. The default is --default_vers 1.5 IMPORTANT: because PRIMER_THERMODYNAMIC_ALIGNMENT=1, PRIMER_THERMODYNAMIC_PARAMETERS_PATH must point to the right location. This tag specifies the path to the directory that contains all the -parameter files used by the thermodynamic approach. In Linux, there +parameter files used by the thermodynamic approach. In Debian, there are two *default* locations that are tested if this tag is not -defined: ./primer3_config/ and /opt/primer3_config/. For Windows, +defined: ./primer3_config/ and /etc/primer3_config/. For Windows, there is only one default location: .\primer3_config\. If the the parameter files are not in one these locations, be sure to set PRIMER_THERMODYNAMIC_PARAMETERS_PATH --- a/primer3_manual.htm +++ b/primer3_manual.htm @@ -229,9 +229,9 @@ defaults. The default is --default_vers 2.5. IMPORTANT: because PRIMER_THERMODYNAMIC_OLIGO_ALIGNMENT=1, PRIMER_THERMODYNAMIC_PARAMETERS_PATH must point to the right location. This tag specifies the path to the directory that contains all the -parameter files used by the thermodynamic approach. In Linux, there +parameter files used by the thermodynamic approach. In Debian, there are two *default* locations that are tested if this tag is not -defined: ./primer3_config/ and /opt/primer3_config/. For Windows, +defined: ./primer3_config/ and /etc/primer3_config/. For Windows, there is only one default location: .\primer3_config\. If the the parameter files are not in one these locations, be sure to set PRIMER_THERMODYNAMIC_PARAMETERS_PATH.
@@ -2452,7 +2452,7 @@ the propensity of oligos to anneal to un

This tag specifies the path to the directory that contains all the parameter files used by the thermodynamic approach. In Linux, there are two default locations that are tested if this tag is not defined: -./primer3_config/ and /opt/primer3_config/. +./primer3_config/ and /etc/primer3_config/. For Windows, there is only one default location: .\primer3_config\.

debian/ntdpal.10000644000000000000000000001023312214301054010521 0ustar '\" t .\" Title: NTDPAL .\" Author: [FIXME: author] [see http://docbook.sf.net/el/author] .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" 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 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 debian/compat0000644000000000000000000000000212214301054010354 0ustar 9 debian/primer3.install0000644000000000000000000000021312254543557012147 0ustar src/primer3_core usr/bin src/ntdpal usr/bin src/ntthal usr/bin src/oligotm usr/bin #src/long_seq_tm_test usr/bin src/primer3_config etc