debian/ 0000755 0000000 0000000 00000000000 12153337166 007175 5 ustar debian/lutefisk-doc.manpages 0000644 0000000 0000000 00000000027 12153337166 013302 0 ustar debian/lutefisk-doc.7
debian/lutefisk.manpages 0000644 0000000 0000000 00000000023 12153337166 012533 0 ustar debian/lutefisk.1
debian/source/ 0000755 0000000 0000000 00000000000 12153337166 010475 5 ustar debian/source/format 0000644 0000000 0000000 00000000015 12153337166 011704 0 ustar 3.0 (quilt)
debian/lutefisk.install 0000644 0000000 0000000 00000000156 12153337166 012415 0 ustar Lutefisk.details usr/share/lutefisk
Lutefisk.residues usr/share/lutefisk
debian/build-arch/lutefisk usr/bin
debian/control 0000644 0000000 0000000 00000002332 12153337166 010600 0 ustar Source: lutefisk
Section: science
Priority: optional
Maintainer: The Debichem Group
Uploaders: Filippo Rusconi
DM-Upload-Allowed: yes
Build-Depends: debhelper (>= 7), dpkg-dev (>= 1.16.1.1)
Standards-Version: 3.9.4
Homepage: http://www.hairyfatguy.com/lutefisk/
Vcs-Git: git://git.debian.org/git/debichem/packages/lutefisk.git
Vcs-Browser: http://git.debian.org/?p=debichem/packages/lutefisk.git
Package: lutefisk
Architecture: any
Depends: ${shlibs:Depends}, ${misc:Depends}
Suggests: lutefisk-doc
Description: de novo interpretation of peptide CID spectra
Lutefisk performs a de novo interpreation of collision-induced decay
(CID) spectra, providing the user with a file containing all the
possible sequence candidates corresponding to the CID data.
Package: lutefisk-doc
Section: doc
Architecture: all
Depends: ${shlibs:Depends}, ${misc:Depends}
Description: De novo interpretation of peptide CID spectra - documentation
Lutefisk performs a de novo interpreation of collision-induced decay
(CID) spectra, providing the user with a file containing all the
possible sequence candidates corresponding to the CID data.
.
This package contains the manual in HTML format.
debian/compat 0000644 0000000 0000000 00000000002 12153337166 010373 0 ustar 7
debian/upstream 0000644 0000000 0000000 00000000751 12153337166 010763 0 ustar Reference:
Author: Richard S. Johnson and J. Alex Taylor
Title: Searching sequence databases via de novo peptide sequencing by tandem mass spectrometry
Journal: Molecular Biotechnology
Year: 2002
Volume: 22
Number: 3
Pages: 301-315
DOI: 10.1385/MB:22:3:301
PMID: 12448884
URL: http://www.springerlink.com/content/3726h1m004207721/
eprint: http://www.springerlink.com/content/3726h1m004207721/fulltext.pdf
Repository : http://sourceforge.net/projects/lutefiskxp/
debian/patches/ 0000755 0000000 0000000 00000000000 12153337166 010624 5 ustar debian/patches/build-flags 0000644 0000000 0000000 00000000422 12153337166 012736 0 ustar Set an incremental CFLAGS flag using += instead of setting it using =
so that the flags in debian/rules are not overwritten.--- a/src/Makefile.linux
+++ b/src/Makefile.linux
@@ -1,5 +1,5 @@
CC= gcc -O
-CFLAGS= -D__LINUX
+CFLAGS+=-D__LINUX
LFLAGS= -lm -o
NRAND= nrand48
debian/patches/series 0000644 0000000 0000000 00000000177 12153337166 012046 0 ustar build-flags
fix-html-doc-paragraph
fix-math-h-include-header
fix-global-definitions
improve-feedback-to-user
fix-pointer-stuff
debian/patches/improve-feedback-to-user 0000644 0000000 0000000 00000012661 12153337166 015354 0 ustar Improve the feedback to the user and make a better implementation of
the usage explanations.--- a/src/LutefiskMain.c
+++ b/src/LutefiskMain.c
@@ -81,6 +81,27 @@
char versionString[256] = "LutefiskXP v1.0.7\nCopyright 1996-1906 Richard S. Johnson\n\n";
+
+static void usage(void)
+{
+ /* print usage */
+ puts("\nUSAGE: lutefisk [options] [CID file pathname]\n");
+ puts( " The following options are available:\n");
+ puts( " -o = output file pathname");
+ puts( " -q = quiet mode ON (default OFF)");
+ puts( " -m = precursor ion mass");
+ puts( " -d = details file pathname");
+ puts( " Default: /usr/share/lutefisk/Lutefisk.details");
+ puts( " -p = params file pathname");
+ puts( " -r = residues file pathname");
+ puts( " Default: /usr/share/lutefisk/Lutefisk.residues");
+ puts( " -s = pathnane of file with database sequences to score");
+ puts( " -v = verbose mode ON (default OFF)");
+ puts( " -h = print this help text");
+ puts( "" );
+ puts("\n");
+}
+
/*
//--------------------------------------------------------------------------------
// main()
@@ -604,82 +625,94 @@
strcpy(gParam.outputFile,"");
- strcpy(gParam.detailsFilename,"Lutefisk.details");
-
- strcpy(gParam.residuesFilename,"Lutefisk.residues");
+ strcpy(gParam.detailsFilename,"/usr/share/lutefisk/Lutefisk.details");
+ strcpy(gParam.residuesFilename,"/usr/share/lutefisk/Lutefisk.residues");
+ /* get command-line parameters */
+
+ if (argc < 2)
+ {
+ usage();
+ exit(1);
+ }
- /* get command-line parameters */
-
- while ((c = getopt(argc, argv, "?hqvd:o:m:p:r:s:")) != -1)
- {
+ while ((c = getopt(argc, argv, "?hqvd:o:m:p:r:s:")) != -1)
+ {
switch (c)
- {
+ {
- case 'o':
+ case 'o':
/* output file name */
- strncpy(gParam.outputFile, optarg, sizeof(gParam.outputFile));
- break;
+ if (memccpy(gParam.outputFile, optarg, '\x0', sizeof(gParam.outputFile)) == NULL)
+ {
+ fprintf(stderr, "Argument filename max length = %d caracters", sizeof(gParam.outputFile) - 1 );
+ exit(1);
+ }
+ break;
- case 'd':
+ case 'd':
/* details file name */
- strncpy(gParam.detailsFilename, optarg, sizeof(gParam.detailsFilename));
+ if (memccpy(gParam.detailsFilename, optarg, '\x0', sizeof(gParam.detailsFilename)) == NULL)
+ {
+ fprintf(stderr, "Argument filename max length = %d caracters", sizeof(gParam.detailsFilename) - 1 );
+ exit(1);
+ }
break;
- case 'm':
+ case 'm':
/* peptide MW */
gParam.peptideMW = atof(optarg);
break;
- case 'p':
+ case 'p':
/* param file name */
- strncpy(gParam.paramFile, optarg, sizeof(gParam.paramFile));
+ if (memccpy(gParam.paramFile, optarg, '\x0', sizeof(gParam.paramFile)) == NULL)
+ {
+ fprintf(stderr, "Argument filename max length = %d caracters", sizeof(gParam.paramFile) - 1 );
+ exit(1);
+ }
break;
- case 'q':
+ case 'q':
/* QUIET! */
gParam.fMonitor = FALSE;
gParam.fVerbose = FALSE;
break;
- case 'r':
- /* residues file name */
- strncpy(gParam.residuesFilename, optarg, sizeof(gParam.residuesFilename));
- break;
-
- case 's':
- /* database sequences file */
- strncpy(gParam.databaseSequences, optarg, sizeof(gParam.databaseSequences));
- break;
-
- case 'v':
+ case 'r':
+ /* residues file name */
+ if (memccpy(gParam.residuesFilename, optarg, '\x0', sizeof(gParam.residuesFilename)) == NULL)
+ {
+ fprintf(stderr, "Argument filename max length = %d caracters", sizeof(gParam.residuesFilename) - 1 );
+ exit(1);
+ }
+ break;
+
+ case 's':
+ /* database sequences file */
+ if (memccpy(gParam.databaseSequences, optarg, '\x0', sizeof(gParam.databaseSequences)) == NULL)
+ {
+ fprintf(stderr, "Argument filename max length = %d caracters", sizeof(gParam.databaseSequences) - 1 );
+ exit(1);
+ }
+ break;
+
+ case 'v':
/* verbose */
gParam.fVerbose = TRUE;
break;
- case '?':
- case 'h':
- /* print usage */
- puts("\nUSAGE: lutefisk [options] [CID file pathname]\n");
- puts( " -o = output file pathname");
- puts( " -q = quiet mode ON (default OFF)");
- puts( " -m = precursor ion mass");
- puts( " -d = details file pathname");
- puts( " -p = params file pathname");
- puts( " -r = residues file pathname");
- puts( " -s = pathnane of file with database sequences to score");
- puts( " -v = verbose mode ON (default OFF)");
- puts( " -h = print this help text");
- puts( "" );
- puts("\n");
- exit(1);
-
- break;
- }
- }
-
+ case '?':
+ case 'h':
+ /* print usage */
+ usage();
+ exit(1);
+
+ break;
+ }
+ }
/* report flag state */
debian/patches/fix-pointer-stuff 0000644 0000000 0000000 00000000663 12153337166 014145 0 ustar Fix some NULL pointer stuff.--- a/src/LutefiskXCorr.c
+++ b/src/LutefiskXCorr.c
@@ -251,7 +251,7 @@
Determine the sequence length.
*/
pSeq = &currScorePtr->peptide[0];
- while(*pSeq != NULL)
+ while(*pSeq != '\x0')
{
seqLength++;
pSeq++;
@@ -552,8 +552,8 @@
*/
pSeq = &currScorePtr->peptide[0];
seqLength = 0;
- while(*pSeq != NULL)
- {
+ while(*pSeq != '\x0')
+ {
seqLength++;
pSeq++;
}
debian/patches/fix-html-doc-paragraph 0000644 0000000 0000000 00000000634 12153337166 015010 0 ustar Small fix to the user html-formatted documentation to better reflect
the location of files on a Debian system.--- a/docs/index.html
+++ b/docs/index.html
@@ -499,7 +499,7 @@
Files
To run Lutefisk, you need to have four
-files within the same directory or folder:
+files:
debian/patches/fix-global-definitions 0000644 0000000 0000000 00000002515 12153337166 015107 0 ustar Improve global definitions.--- a/src/LutefiskDefinitions.h
+++ b/src/LutefiskDefinitions.h
@@ -143,6 +143,7 @@
#define BOOLEAN unsigned char
#endif
+#define MAX_FILENAME_SIZE 4096
/* Define a few constants. */
#define AMINO_ACID_NUMBER 25 /*Number of amino acids.*/
@@ -357,11 +358,11 @@
char fVerbose;
clock_t startTicks;
clock_t searchTime;
- char paramFile[256];
- char outputFile[256];
- char cidFilename[256];
- char detailsFilename[256];
- char residuesFilename[256];
+ char paramFile[MAX_FILENAME_SIZE];
+ char outputFile[MAX_FILENAME_SIZE];
+ char cidFilename[MAX_FILENAME_SIZE];
+ char detailsFilename[MAX_FILENAME_SIZE];
+ char residuesFilename[MAX_FILENAME_SIZE];
REAL_4 peptideMW;
INT_4 chargeState;
BOOLEAN maxent3;
@@ -395,10 +396,10 @@
REAL_4 peptideErr;
BOOLEAN autoTag;
BOOLEAN edmanPresent;
- char edmanFilename[256];
+ char edmanFilename[MAX_FILENAME_SIZE];
REAL_4 ionsPerResidue;
char CIDfileType;
- char databaseSequences[256];
+ char databaseSequences[MAX_FILENAME_SIZE];
BOOLEAN quality;
INT_4 wrongSeqNum;
@@ -416,7 +417,7 @@
REAL_4 modifiedNTerm_orig;
REAL_4 modifiedCTerm_orig;
INT_4 maxGapNum_orig;
- char outputFile_orig[256];
+ char outputFile_orig[MAX_FILENAME_SIZE];
}tParam;
debian/patches/fix-math-h-include-header 0000644 0000000 0000000 00000001067 12153337166 015364 0 ustar Add #include statements.--- a/src/LutefiskHaggis.c
+++ b/src/LutefiskHaggis.c
@@ -34,6 +34,7 @@
#include
#include
#include
+#include
/* Haggis headers */
#include "LutefiskPrototypes.h"
@@ -2275,4 +2276,4 @@
}
}
return;
-}
\ No newline at end of file
+}
--- a/src/LutefiskMain.c
+++ b/src/LutefiskMain.c
@@ -52,6 +52,7 @@
#include
#include
#include
+#include
#if(defined(__MWERKS__) && __dest_os == __mac_os)
/* Some Macintosh specific things */
debian/lutefisk-doc.install 0000644 0000000 0000000 00000000042 12153337166 013152 0 ustar docs /usr/share/doc/lutefisk-doc
debian/lutefisk.1 0000644 0000000 0000000 00000005562 12153337166 011115 0 ustar .TH "LUTEFISK" "1" "2009/04/29" "" ""
.SH "NAME"
lutefisk \- software for the de novo interpretation of peptide CID spectra
.SH "SYNOPSIS"
\fBlutefisk\fR [\-q ] [ \-m ] [ \-d] [ \-p ] [ \-r ] [ \-s ] [ \-v] [ \-h] [\-o ]
.SH "DESCRIPTION"
\fBlutefisk\fR is a software for the de novo interpretation of peptide
CID spectra. It takes peptide CID data and some ancillary data files
(of which the location is specified on the command line) and outputs a
results file containing all the sequences hypothetically matching the
CID data.
When you invoke \fBlutefisk\fR with the \fB\-h\fR option, the program
lists to the command line all the options that are available.
.SH "OPTIONS"
.TP
.B \-h
Print a list of options
.TP
.B \-q
Run in quiet mode
.TP
.B \-m
Precursor ion mass
.TP
.B \-d
Pathname to the details file
.TP
.B \-p
Pathname to the params file
.TP
.B \-r
Pathname to the residues file
.TP
.B \-s
Pathname to the file with database sequences to score
.TP
.B \-v
Run in verbose mode
.TP
.B \-o
Output file
.TP
.B
CID data file
.SH "PROGRAM DATA"
The data required to run the program are located in \fI\%/usr/share/lutefisk\fP.
.SH "EXAMPLE DATA"
Example data are located in \fI\%/usr/share/doc/lutefisk/examples\fP.
.SH "BIBLIOGRAPHICAL REFERENCES TO BE CITED"
R. S. Johnson and J. A. Taylor (2002) "Searching sequence databases
via de novo peptide sequencing by tandem mass spectrometry",
Mol. Biotechnology Vol. 22, No. 3. (November 2002), pp. 301\-315.
.PP
J. A. Taylor and R. S. Johnson (2000) "Implementation and uses of
automated de novo peptide sequencing by tandem mass
spectrometry". Anal. Chem. 73:2594\-2604.
.PP
R. S. Johnson and J. A. Taylor (2000) "Searching sequence databases
via de novo peptide sequencing by tandem mass spectrometry", "Protein
and Peptide Analysis: Advances in the Use of Mass Spectrometry",
146:41\-61 (Methods in Molecular Biology series, Humana Press).
.PP
J. A. Taylor and R. S. Johnson (1997) "Sequence database searches via
de novo peptide sequencing by tandem mass spectrometry". Rapid
Comm. Mass Spec. 11:1067-1075.
.SH "SEE ALSO"
.BR lutefisk\-doc (7).
.SH "AUTHORS"
\fB Richard S. Johnson\fR <\&jsrichar@alum.mit.edu\&>.
.sp -1n
.IP "" 4
Program author.
.PP
\fBFilippo Rusconi\fR <\&rusconi\-debian@laposte.net\&>.
.sp -1n
.IP "" 4
Man\-page author for the Debian distribution\&.
.SH "COPYRIGHT"
Copyright \(co 1995\-1999 Richard S. Johnson
.PP
Copyright \(co 2009 Filippo Rusconi
.PP
This manual page was written for the Debian system (but may be used by others).
.PP
Permission is granted to copy, distribute and/or modify this document
under the terms of the GNU General Public License, Version 3 or (at
your option) any later version published by the Free Software
Foundation\&.
.PP
On a Debian system the complete text of the GNU General Public
License version 3 can be found in the file
`\fI\%/usr/share/common-licenses/GPL\-3\fP'.
debian/copyright 0000644 0000000 0000000 00000006272 12153337166 011137 0 ustar This package was debianized by Filippo Rusconi on
Wed, 13 May 2009 18:48:36 +0200.
It was downloaded from http://sourceforge.net/projects/lutefiskxp/
Author: Richard S. Johnson
Lutefisk Copyright © 1995-1999 Richard S. Johnson
License for Lutefisk: GNU General Public License
This program is free software; you can redistribute it and/or
modify it 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 program 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 program; if not, write to the Free Software
Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA
02110-1301, USA.
On Debian systems, the GNU General Public License, is available as
the file `/usr/share/common-licenses/GPL-2'.
License for Lutefisk documentation files: GNU General Public License
Although the main documentation file has the following two lines
Copyright © 2005 Rich Johnson (jsrichar@alum.mit.edu)
All rights reserved worldwide
the documentation is under GPLv2, as shown in the transcript of mails
exchanged with the upstream author.
~~~~~~~~~~~~~~~~~~~~~~~~ BEGIN TRANSCRIPT ~~~~~~~~~~~~~~~~~~~~~~~~
From toxothurston@gmail.com Thu Apr 30 07:45:12 2009
In-Reply-To: <20090428162709.GE3730@biophypfr>
References: <20090428162709.GE3730@biophypfr>
Date: Wed, 29 Apr 2009 17:37:43 -0700
Message-ID:
Subject: Re: Lutefisk enquiry, specifically the documentation
From: Richard Johnson
To: Filippo Rusconi
Yes, its all under the same license.
Rich
On Tue, Apr 28, 2009 at 9:27 AM, Filippo Rusconi wrote:
> Greetings,
>
> I am starting the packaging of Lutefisk for GNU/Linux (Debian,
> specifically). I would also like to package the documentation, as the
> set of files that come along with the source tarball. Could you please
> tell me if the docs/* files are all under the same license as the
> program itself (GPL v2)?
>
> Thank you for choosing the GPL for publishing your work.
>
> Sincerely, Filippo
>
> --
> Filippo Rusconi, PhD - CNRS - public key C78F687C
> Author of ``massXpert'' at http://www.massxpert.org
>
> -----BEGIN PGP SIGNATURE-----
> Version: GnuPG v1.4.9 (GNU/Linux)
>
> iEYEARECAAYFAkn3Ll0ACgkQTTOs5MePaHwxmACffAUYh8AmoCIyhypXBnPrr5L/
> UNoAoKErhXRK/ssTzRo2jHbVTfU1t1I8
> =g+of
> -----END PGP SIGNATURE-----
~~~~~~~~~~~~~~~~~~~~~~ END TRANSCRIPT ~~~~~~~~~~~~~~~~~~~~~~
The Debian packaging is © 2009 Filippo Rusconi and
is licensed under the GPL, see `/usr/share/common-licenses/GPL-3'.
debian/rules 0000755 0000000 0000000 00000004263 12153337166 010262 0 ustar #!/usr/bin/make -f
# Based on the initial work of Joey Hess and Craig Small.
# Uncomment this to turn on verbose mode.
export DH_VERBOSE=1
DEB_HOST_GNU_TYPE ?= $(shell dpkg-architecture -qDEB_HOST_GNU_TYPE)
DEB_BUILD_GNU_TYPE ?= $(shell dpkg-architecture -qDEB_BUILD_GNU_TYPE)
PACKAGE=lutefisk
BUILD_DIR = $(CURDIR)/debian/build-arch
ifneq (,$(filter parallel=%,$(DEB_BUILD_OPTIONS)))
NUMJOBS = $(patsubst parallel=%,%,$(filter parallel=%,$(DEB_BUILD_OPTIONS)))
MAKEFLAGS += -j$(NUMJOBS)
endif
$(info "---------------------------------------")
$(info NUMJOBS: $(NUMJOBS))
$(info MAKEFLAGS: $(MAKEFLAGS))
$(info DEB_BUILD_OPTIONS: $(DEB_BUILD_OPTIONS))
$(info "---------------------------------------")
# Hardening stuff, see http://wiki.debian.org/Hardening
# export DEB_BUILD_MAINT_OPTIONS = hardening=+all
# DPKG_EXPORT_BUILDFLAGS = 1
# include /usr/share/dpkg/buildflags.mk
# $(info CFLAGS: $(CFLAGS))
# Uncomment to monitor the log of package building (pdebuild log)
# .NOTPARALLEL:
.PHONY: clean
clean:
dh_testdir
dh_testroot
dh_clean
rm -rf $(BUILD_DIR)
configure-stamp:
dh_testdir
mkdir -p $(BUILD_DIR)
cp -rpf src/* $(BUILD_DIR)
ln -s $(BUILD_DIR)/Makefile.linux $(BUILD_DIR)/Makefile
touch configure-stamp
.PHONY: build
build: build-indep build-arch
.PHONY: build-indep
build-indep:
.PHONY: build-arch
build-arch: build-arch-stamp
build-arch-stamp: configure-stamp
dh_testdir
dh_prep -a
cd $(BUILD_DIR) && $(MAKE) all
touch build-arch-stamp
# Build architecture-independent files here.
.PHONY: binary-indep
binary-indep:
dh_testdir -i
dh_testroot -i
dh_installchangelogs HISTORY.txt -i
dh_installdocs -i
dh_install -i
dh_installman -i
dh_compress -i
dh_fixperms -i
dh_installdeb -i
dh_gencontrol -i
dh_md5sums -i
dh_builddeb -i
# Build architecture-dependent files here.
.PHONY: binary-arch
binary-arch: build-arch
dh_testdir -a
dh_testroot -a
dh_installchangelogs HISTORY.txt -a
dh_installdocs -a
dh_installexamples -a
dh_install -a
dh_installman -a
dh_strip -a
dh_compress -a
dh_fixperms -a
dh_installdeb -a
dh_shlibdeps -a
dh_gencontrol -a
dh_md5sums -a
dh_builddeb -a
.PHONY: binary
binary: binary-indep binary-arch
debian/get-orig-source.sh 0000755 0000000 0000000 00000001454 12153337166 012553 0 ustar #!/bin/sh
set -ex
UPSTREAM_VERSION=$2
ORIG_TARBALL=$3
REAL_TARBALL=`readlink -f ${ORIG_TARBALL}`
WORKING_DIR=`dirname ${ORIG_TARBALL}`
ORIG_TARBALL_DFSG=`echo ${ORIG_TARBALL} | sed -e "s/\(${UPSTREAM_VERSION}\)\(\.orig\)/\1+dfsg\2/g"`
ORIG_TARBALL_DIR=`echo ${ORIG_TARBALL_DFSG} | sed -e "s/_\(${UPSTREAM_VERSION}\)/-\1/g" -e "s/\.tar\.gz//g"`
ORIG_TARBALL_DIR_STRIP=`basename ${ORIG_TARBALL_DIR}`
mkdir -p ${ORIG_TARBALL_DIR}
tar --directory=${ORIG_TARBALL_DIR} --strip 1 -xzf ${REAL_TARBALL} || exit 1
rm -f ${ORIG_TARBALL} ${REAL_TARBALL}
rm -rf ${ORIG_TARBALL_DIR}/windoze/
mv -f "${ORIG_TARBALL_DIR}/docs/LutefiskXP Operators Manual.htm" "${ORIG_TARBALL_DIR}/docs/index.html"
GZIP=-9 tar --remove-files --directory ${WORKING_DIR} -czf ${ORIG_TARBALL_DFSG} ${ORIG_TARBALL_DIR_STRIP} || exit 1
exit 0
debian/lutefisk-doc.7 0000644 0000000 0000000 00000002515 12153337166 011661 0 ustar .TH "LUTEFISK" "7" "2009/04/25" "" ""
.SH "NAME"
lutefisk-doc \- software for the de novo interpretation of peptide
CID spectra (documentation)
.SH "DESCRIPTION"
This manual page documents briefly the \fBlutefisk\-doc\fR package. This
package contains the user manual for the \fBlutefisk\fR software
package. The documentation is provided in the form of a set of HTML
files. The files are located in /usr/share/doc/lutefisk\-doc. Note that
the documentation is also available at
\fI\%http://www.hairyfatguy.com/lutefisk/docs/\fP.
.SH "SEE ALSO"
.BR lutefisk (1).
.SH "AUTHORS"
\fB Richard S. Johnson\fR <\&jsrichar@alum.mit.edu\&>.
.sp -1n
.IP "" 4
Program author.
.PP
\fBFilippo Rusconi\fR <\&rusconi\-debian@laposte.net\&>.
.sp -1n
.IP "" 4
Man\-page author for the Debian distribution\&.
.SH "COPYRIGHT"
Copyright \(co 1995\-1999 Richard S. Johnson
.PP
Copyright \(co 2009 Filippo Rusconi
.PP
This manual page was written for the Debian system (but may be used by others).
.PP
Permission is granted to copy, distribute and/or modify this document
under the terms of the GNU General Public License, Version 3 or (at
your option) any later version published by the Free Software
Foundation\&.
.PP
On a Debian system the complete text of the GNU General Public
License version 3 can be found in the file
`\fI\%/usr/share/common-licenses/GPL\-3\fP'.
debian/lutefisk.dirs 0000644 0000000 0000000 00000000011 12153337166 011676 0 ustar usr/bin
debian/watch 0000644 0000000 0000000 00000000217 12153337166 010226 0 ustar version=3
opts=dversionmangle=s/\+dfsg$// \
http://sf.net/lutefiskxp/LutefiskXPv([\d.]+)\.tar\.gz \
debian /bin/sh debian/get-orig-source.sh
debian/lutefisk-doc.doc-base 0000644 0000000 0000000 00000000554 12153337166 013171 0 ustar Document: lutefisk-documentation
Title: lutefisk
Author: Richard S. Johnson
Abstract: This manual describes what lutefisk is and how it can be used
to perform de novo interpretations of peptide CID spectra.
Section: Science/Chemistry
Format: HTML
Index: /usr/share/doc/lutefisk-doc/docs/index.html
Files: /usr/share/doc/lutefisk-doc/docs
debian/changelog 0000644 0000000 0000000 00000003551 12153337166 011053 0 ustar lutefisk (1.0.7+dfsg-1) unstable; urgency=low
* new upstream version;
* applied patches as for previous version, but this time using the
dquilt setup. For that set the source format to 3.0 (quilt);
* debian/control: Standards-Version: 3.9.4 and set address to
lopippo@debian.org;
* set the basis for hardening stuff but commented out because would
require a lot of work. I let that for another release;
* set dpkg-dev (>= 1.16.1.1) to build depends for hardening stuff;
* debian/watch: new version of watch file from kind contribution of
Daniel Leidert ;
* debian/get-orig-source.sh: script to get the original source, clean it
and make an orig tarball. Kind contribution from Daniel;
Leidert. (Closes: #675830; sorry Daniel that I somehow skipped the bug
report for so long);
* change debian/get-orig-source.sh so that awful doc file name is moved
to index.html;
* debian/rules: remove the renaming of the doc file since performed at
orig tarball constitution.
-- Filippo Rusconi Tue, 04 Jun 2013 12:06:36 +0200
lutefisk (1.0.5a.cleaned-1) unstable; urgency=low
* Initial release (Closes: #527141);
* Removed file windoze/lutefisk.exe that was shipped in the upstream
tarball;
* Fixed glitches in the upstream source that had gcc emit warning
(#include in two files and and replace 'NULL' with '\x0' to
test end of array in one file);
* Move the main HTML documentation file (space-ridden filename) to
index.html;
* Look for default files in /usr/share/lutefisk/, not current directory.
* Display usage help when no argument given.
* Protect against too long filenames (and raise the limit).
* Sponsored upload done by Lionel Elie Mamane .
-- Filippo Rusconi Wed, 09 Dec 2009 22:42:38 +0100
debian/lutefisk.examples 0000644 0000000 0000000 00000000146 12153337166 012564 0 ustar database.sequence
Lutefisk.lcq_params
Lutefisk.qtof_params
Qtof_ELVISLIVESK.dta
Qtof_ELVISLIVESK.lut