[med-svn] r834 - trunk/packages/primer3/trunk/debian
hanska-guest at alioth.debian.org
hanska-guest at alioth.debian.org
Sun Nov 18 10:55:51 UTC 2007
Author: hanska-guest
Date: 2007-11-18 10:55:51 +0000 (Sun, 18 Nov 2007)
New Revision: 834
Added:
trunk/packages/primer3/trunk/debian/ntdpal.1
trunk/packages/primer3/trunk/debian/oligotm.1
trunk/packages/primer3/trunk/debian/primer3_core.1
Modified:
trunk/packages/primer3/trunk/debian/changelog
trunk/packages/primer3/trunk/debian/control
trunk/packages/primer3/trunk/debian/rules
Log:
* 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
* debian/rules:
- manpages statically built
- minor changes
Modified: trunk/packages/primer3/trunk/debian/changelog
===================================================================
--- trunk/packages/primer3/trunk/debian/changelog 2007-11-18 10:45:10 UTC (rev 833)
+++ trunk/packages/primer3/trunk/debian/changelog 2007-11-18 10:55:51 UTC (rev 834)
@@ -1,9 +1,20 @@
-primer3 (1.1.1-2) unreleased; urgency=low
+primer3 (1.1.1-2) UNRELEASED; urgency=low
+ [ Charles Plessy ]
* Moved the Homepage: field out from the package's description.
- -- Charles Plessy <charles-debian-nospam at plessy.org> Fri, 21 Sep 2007 23:20:58 +0900
+ [ 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
+ * debian/rules:
+ - manpages statically built
+ - minor changes
+ -- David Paleino <d.paleino at gmail.com> Sun, 18 Nov 2007 11:54:24 +0100
+
primer3 (1.1.1-1) unstable; urgency=low
* New upstream release.
Modified: trunk/packages/primer3/trunk/debian/control
===================================================================
--- trunk/packages/primer3/trunk/debian/control 2007-11-18 10:45:10 UTC (rev 833)
+++ trunk/packages/primer3/trunk/debian/control 2007-11-18 10:55:51 UTC (rev 834)
@@ -2,8 +2,10 @@
Section: science
Priority: optional
Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Steffen Moeller <steffen_moeller at gmx.de>, Charles Plessy <charles-debian-nospam at plessy.org>
-Build-Depends: debhelper (>= 5), xsltproc, docbook-xsl, docbook-xml
+Uploaders: Steffen Moeller <steffen_moeller at gmx.de>,
+ Charles Plessy <charles-debian-nospam at plessy.org>,
+ David Paleino <d.paleino at gmail.com>
+Build-Depends: debhelper (>= 5)
Standards-Version: 3.7.2
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/primer3/trunk/
Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/primer3
Added: trunk/packages/primer3/trunk/debian/ntdpal.1
===================================================================
--- trunk/packages/primer3/trunk/debian/ntdpal.1 (rev 0)
+++ trunk/packages/primer3/trunk/debian/ntdpal.1 2007-11-18 10:55:51 UTC (rev 834)
@@ -0,0 +1,112 @@
+.\" Title: NTDPAL
+.\" Author:
+.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
+.\" Date: February 17, 2007
+.\" Manual: Primer3 User Manuals
+.\" Source: ntdpal 1.1.1
+.\"
+.TH "NTDPAL" "1" "February 17, 2007" "ntdpal 1.1.1" "Primer3 User Manuals"
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.SH "NAME"
+ntdpal - Provides Primer3's alignment functionality
+.SH "SYNOPSIS"
+.HP 7
+\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\'s 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 penaltiy 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 penaltiy 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 postion of the alignment in both sequences to be printed\. Do not confuse with the \'e\'
+\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\-achored 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"
+Copyright \(co 1996,1997,1998,1999,2000,2001,2004,2006,2007 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 ntdpal\.
+.PP
+This manual page was written by Charles Plessy
+<charles\-debian\-nospam at plessy\.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
Added: trunk/packages/primer3/trunk/debian/oligotm.1
===================================================================
--- trunk/packages/primer3/trunk/debian/oligotm.1 (rev 0)
+++ trunk/packages/primer3/trunk/debian/oligotm.1 2007-11-18 10:55:51 UTC (rev 834)
@@ -0,0 +1,114 @@
+.\" Title: OLIGOTM
+.\" Author:
+.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
+.\" Date: February 17, 2007
+.\" Manual: Primer3 User Manuals
+.\" Source: oligotm 1.1.1
+.\"
+.TH "OLIGOTM" "1" "February 17, 2007" "oligotm 1.1.1" "Primer3 User Manuals"
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.SH "NAME"
+oligotm - Prints oligo's melting temperature on stdout
+.SH "SYNOPSIS"
+.HP 8
+\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 desoxyribooligonucleotide 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 deoxynycleotide 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
+\h'-04'\(bu\h'+03'\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
+\h'-04'\(bu\h'+03'\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
+\h'-04'\(bu\h'+03'\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
+\h'-04'\(bu\h'+03'\fI1\fR
+SantaLucia 1998\.
+\fIThis is the recommended value\fR\.
+.RE
+.sp
+.RS 4
+\h'-04'\(bu\h'+03'\fI1\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"
+Copyright \(co 1996,1997,1998,1999,2000,2001,2004,2006,2007 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 oligotm\.
+.PP
+This manual page was written by Charles Plessy
+<charles\-debian\-nospam at plessy\.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
Added: trunk/packages/primer3/trunk/debian/primer3_core.1
===================================================================
--- trunk/packages/primer3/trunk/debian/primer3_core.1 (rev 0)
+++ trunk/packages/primer3/trunk/debian/primer3_core.1 2007-11-18 10:55:51 UTC (rev 834)
@@ -0,0 +1,90 @@
+.\" Title: PRIMER3_CORE
+.\" Author:
+.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
+.\" Date: February 17, 2007
+.\" Manual: Primer3 User Manuals
+.\" Source: primer3_core 1.1.1
+.\"
+.TH "PRIMER3_CORE" "1" "February 17, 2007" "primer3_core 1.1.1" "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 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
+<steffen_moeller at gmx\.de>
+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
Modified: trunk/packages/primer3/trunk/debian/rules
===================================================================
--- trunk/packages/primer3/trunk/debian/rules 2007-11-18 10:45:10 UTC (rev 833)
+++ trunk/packages/primer3/trunk/debian/rules 2007-11-18 10:55:51 UTC (rev 834)
@@ -22,22 +22,24 @@
PRIMER_EXE = primer3_core
EXES=$(PRIMER_EXE) ntdpal oligotm long_seq_tm_test
-build: manpages
+XP=xsltproc -o debian/ -''-nonet
+DB2MAN=/usr/share/xml/docbook/stylesheet/nwalsh/manpages/docbook.xsl
+
+
+build: build-stamp
+build-stamp:
dh_testdir
$(MAKE) -C src all
- touch build-stamp
+ touch $@
-build-stamp: build
-
-tests-stamp: tests
-
-tests: build-stamp tests-clean
+tests: build tests-clean tests-stamp
+tests-stamp:
ifeq (,$(filter $(DEB_HOST_ARCH_CPU),$(SKIP_TEST_CPUS)))
$(MAKE) -C test test
else
@echo "Slow-cpu arch detected, skipping test"
endif
- touch tests-stamp
+ touch $@
tests-clean:
$(MAKE) -C test clean
@@ -51,19 +53,18 @@
# make clean fails on clean sources, so I clean with this:
# cd src ; rm -f *.o $(EXES) *~
- dh_clean debian/primer3_core.1 debian/ntdpal.1 debian/oligotm.1 debian/manpages
+ dh_clean
-debian/primer3_core.1: debian/primer3_core.1.xml
- xsltproc -o debian/ -''-nonet /usr/share/xml/docbook/stylesheet/nwalsh/manpages/docbook.xsl $<
+primer3_core.1: debian/primer3_core.1.xml
+ $(XP) $(DB2MAN) $<
-debian/ntdpal.1: debian/ntdpal.1.xml
- xsltproc -o debian/ -''-nonet /usr/share/xml/docbook/stylesheet/nwalsh/manpages/docbook.xsl $<
+ntdpal.1: debian/ntdpal.1.xml
+ $(XP) $(DB2MAN) $<
-debian/oligotm.1: debian/oligotm.1.xml
- xsltproc -o debian/ -''-nonet /usr/share/xml/docbook/stylesheet/nwalsh/manpages/docbook.xsl $<
+oligotm.1: debian/oligotm.1.xml
+ $(XP) $(DB2MAN) $<
-manpages: debian/primer3_core.1 debian/ntdpal.1 debian/oligotm.1
- touch debian/manpages
+manpages: primer3_core.1 ntdpal.1 oligotm.1
install: build
dh_testdir
@@ -71,7 +72,6 @@
dh_clean -k
dh_installdirs
-# Build architecture-dependent files here.
binary-arch: build install tests-stamp
dh_testdir
dh_testroot
@@ -93,4 +93,4 @@
binary-indep:
binary: binary-arch
-.PHONY: build clean binary-arch binary install configure
+.PHONY: build clean binary-arch binary install
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