[med-svn] r1575 - in trunk/packages: . coils coils/trunk coils/trunk/debian coils/trunk/debian/patches
tille at alioth.debian.org
tille at alioth.debian.org
Thu Mar 13 11:43:06 UTC 2008
Author: tille
Date: 2008-03-13 11:43:06 +0000 (Thu, 13 Mar 2008)
New Revision: 1575
Added:
trunk/packages/coils/
trunk/packages/coils/trunk/
trunk/packages/coils/trunk/README
trunk/packages/coils/trunk/debian/
trunk/packages/coils/trunk/debian/README.Debian
trunk/packages/coils/trunk/debian/changelog
trunk/packages/coils/trunk/debian/compat
trunk/packages/coils/trunk/debian/control
trunk/packages/coils/trunk/debian/copyright
trunk/packages/coils/trunk/debian/dirs
trunk/packages/coils/trunk/debian/docs
trunk/packages/coils/trunk/debian/ncoils.1
trunk/packages/coils/trunk/debian/patches/
trunk/packages/coils/trunk/debian/patches/xyz.diff
trunk/packages/coils/trunk/debian/rules
Log:
Moved Steffen M?\195?\182llers work which was stalled to svn to keep track of previous work.
Added: trunk/packages/coils/trunk/README
===================================================================
--- trunk/packages/coils/trunk/README (rev 0)
+++ trunk/packages/coils/trunk/README 2008-03-13 11:43:06 UTC (rev 1575)
@@ -0,0 +1,3 @@
+Work on this project was started by Steffen Möller but has stalled.
+Feel free to take it over.
+
Added: trunk/packages/coils/trunk/debian/README.Debian
===================================================================
--- trunk/packages/coils/trunk/debian/README.Debian (rev 0)
+++ trunk/packages/coils/trunk/debian/README.Debian 2008-03-13 11:43:06 UTC (rev 1575)
@@ -0,0 +1,20 @@
+coils for Debian
+----------------
+
+The software has no version specified. It is said
+to be the same algorithm as published in
+
+ Lupas, van Dyke & Stock
+ Predicting coiled coils from protein sequences Science
+ 252:1162-1164(1991)
+
+The web server is not prepared in this Debian package. A
+separate package will be prepared upon respective requests
+for the CGI. The perl scripts are distributed in
+/usr/share/doc/coils.
+
+The source was last modified in 2002, hence the version, as no other
+version information was found.
+
+ -- Steffen Moeller <moeller at pzr.uni-rostock.de>
+
Added: trunk/packages/coils/trunk/debian/changelog
===================================================================
--- trunk/packages/coils/trunk/debian/changelog (rev 0)
+++ trunk/packages/coils/trunk/debian/changelog 2008-03-13 11:43:06 UTC (rev 1575)
@@ -0,0 +1,6 @@
+coils (2002-0.1) unstable; urgency=low
+
+ * Initial Release.
+
+ -- Steffen Moeller <moeller at pzr.uni-rostock.de> Wed, 16 Mar 2005 23:21:37 +0100
+
Added: trunk/packages/coils/trunk/debian/compat
===================================================================
--- trunk/packages/coils/trunk/debian/compat (rev 0)
+++ trunk/packages/coils/trunk/debian/compat 2008-03-13 11:43:06 UTC (rev 1575)
@@ -0,0 +1 @@
+4
Added: trunk/packages/coils/trunk/debian/control
===================================================================
--- trunk/packages/coils/trunk/debian/control (rev 0)
+++ trunk/packages/coils/trunk/debian/control 2008-03-13 11:43:06 UTC (rev 1575)
@@ -0,0 +1,18 @@
+Source: coils
+Section: science
+Priority: optional
+Maintainer: Steffen Moeller <moeller at pzr.uni-rostock.de>
+Build-Depends: debhelper (>= 4.0.0)
+Standards-Version: 3.6.1
+
+Package: ncoils
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Suggested: gnuplot
+Description: [Biology] coiled coil secondary structure prediction
+ The program predicts the coiled coil secondary structure predictions
+ from protein sequences. The algorithm was published in
+ Lupas, van Dyke & Stock, Predicting coiled coils from
+ protein sequences Science, 252, 1162-1164, 1991.
+ .
+ Homepage: http://www.russell.embl.de/cgi-bin/coils-svr.pl
Added: trunk/packages/coils/trunk/debian/copyright
===================================================================
--- trunk/packages/coils/trunk/debian/copyright (rev 0)
+++ trunk/packages/coils/trunk/debian/copyright 2008-03-13 11:43:06 UTC (rev 1575)
@@ -0,0 +1,28 @@
+This package was debianized by Steffen Moeller <moeller at pzr.uni-rostock.de> on
+Wed Mar 16 23:57:06 CET 2005.
+
+It was downloaded from <http://www.russell.embl-heidelberg.de/coils/coils.tar.gz>
+
+Copyright:
+
+Upstream Author: Rob Russel <russell at embl.de>
+
+License:
+
+ This package 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; version 2 dated June, 1991.
+
+ This package 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 package; if not, write to the Free Software
+ Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA
+ 02111-1307, USA.
+
+On Debian systems, the complete text of the GNU General
+Public License can be found in `/usr/share/common-licenses/GPL'.
+
Added: trunk/packages/coils/trunk/debian/dirs
===================================================================
--- trunk/packages/coils/trunk/debian/dirs (rev 0)
+++ trunk/packages/coils/trunk/debian/dirs 2008-03-13 11:43:06 UTC (rev 1575)
@@ -0,0 +1,2 @@
+usr/bin
+usr/share/ncoils
Added: trunk/packages/coils/trunk/debian/docs
===================================================================
--- trunk/packages/coils/trunk/debian/docs (rev 0)
+++ trunk/packages/coils/trunk/debian/docs 2008-03-13 11:43:06 UTC (rev 1575)
@@ -0,0 +1 @@
+README
Added: trunk/packages/coils/trunk/debian/ncoils.1
===================================================================
--- trunk/packages/coils/trunk/debian/ncoils.1 (rev 0)
+++ trunk/packages/coils/trunk/debian/ncoils.1 2008-03-13 11:43:06 UTC (rev 1575)
@@ -0,0 +1,26 @@
+.\" Hey, EMACS: -*- nroff -*-
+.TH COILS 1 "March 16, 2005"
+.\" Please adjust this date whenever revising the manpage.
+.\"
+.\" Some roff macros, for reference:
+.\" .nh disable hyphenation
+.\" .hy enable hyphenation
+.\" .ad l left justify
+.\" .ad b justify to both left and right margins
+.\" .nf disable filling
+.\" .fi enable filling
+.\" .br insert line break
+.\" .sp <n> insert n+1 empty lines
+.\" for manpage-specific macros, see man(7)
+.SH NAME
+ncoils \- prediction of coiled-coil secondary structure elements
+.SH SYNOPSIS
+.B ncoils
+-f < sequence.fasta
+.SH SEE ALSO
+.BR /usr/share/doc/coils/README
+.br
+.BR http://www.russell.embl.de/cgi-bin/coils-svr.pl
+.br
+.SH AUTHOR
+coils was written by Rob Russel.
Added: trunk/packages/coils/trunk/debian/patches/xyz.diff
===================================================================
--- trunk/packages/coils/trunk/debian/patches/xyz.diff (rev 0)
+++ trunk/packages/coils/trunk/debian/patches/xyz.diff 2008-03-13 11:43:06 UTC (rev 1575)
@@ -0,0 +1,68 @@
+--- coils-2002.orig/ncoils.h
++++ coils-2002/ncoils.h
+@@ -1,5 +1,6 @@
+ #include <stdio.h>
+ #include <stdlib.h>
++#include <string.h>
+ #include <math.h>
+
+ #define AAs "A_CDEFGHI_KLMN_PQRST_VW_Y_"
+--- coils-2002.orig/ncoils.c
++++ coils-2002/ncoils.c
+@@ -23,7 +23,7 @@
+
+ /* Rob Russell's attempt to make a COILS program */
+
+-main(int argc, char *argv[]) {
++int main(int argc, char *argv[]) {
+
+ int i,j,k,l;
+ int verb;
+@@ -31,14 +31,16 @@
+ int which,weighted;
+ int nseq;
+ int t,tc;
+- int seqlen;
++ int seqlen=0;
+ int mode;
+ int min_seg;
+
+ char heptfile[1000];
+ char *buff;
+ static char *env;
+- char *seq,*title,*ident;
++ char *seq =(char *) NULL,
++ *title=(char *) NULL,
++ *ident=(char *) NULL;
+
+ float min_P;
+
+@@ -55,13 +57,13 @@
+ min_P = 0.5;
+
+ if((env=getenv("COILSDIR"))==NULL) {
+- fprintf(stderr,"error: environment variable COILSDIR must be set\n");
+- exit(-1);
++ fprintf(stderr,"warning: environment variable COILSDIR not set, assuming /usr/share/ncoils/\n");
++ strcpy(heptfile,"/usr/share/ncoils/new.mat");
++ } else {
++ strncpy(&heptfile[0],env,990);
++ strcpy(&heptfile[strlen(heptfile)],"/new.mat");
+ }
+
+- strcpy(&heptfile[0],env);
+- strcpy(&heptfile[strlen(heptfile)],"/new.mat");
+-
+
+ for(i=1; i<argc; ++i) {
+ if(argv[i][0]!='-') exit_error();
+@@ -171,8 +173,7 @@
+ fprintf(stderr,"%8d sequences %8d aas %8d in coil\n",nseq,t,tc);
+ free(title); free(ident);
+
+- exit(0);
+-
++ return(0);
+ }
+
+ void exit_error() {
Added: trunk/packages/coils/trunk/debian/rules
===================================================================
--- trunk/packages/coils/trunk/debian/rules (rev 0)
+++ trunk/packages/coils/trunk/debian/rules 2008-03-13 11:43:06 UTC (rev 1575)
@@ -0,0 +1,73 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+# Sample debian/rules that uses debhelper.
+# This file was originally written by Joey Hess and Craig Small.
+# As a special exception, when this file is copied by dh-make into a
+# dh-make output file, you may use that output file without restriction.
+# This special exception was added by Craig Small in version 0.37 of dh-make.
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+
+CC = gcc
+
+CFLAGS = -Wall -g
+
+ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS)))
+ CFLAGS += -O0
+else
+ CFLAGS += -O2
+endif
+
+build: build-stamp
+
+build-stamp:
+ dh_testdir
+
+ # Add here commands to compile the package.
+ $(CC) $(CFLAGS) -I. -o ncoils ncoils.c read_matrix.c -lm
+
+ touch build-stamp
+
+clean:
+ dh_testdir
+ dh_testroot
+ rm -f build-stamp configure-stamp
+
+ # Add here commands to clean up after the build process.
+ dh_clean ncoils
+
+install: build
+ dh_testdir
+ dh_testroot
+ dh_clean -k
+ dh_installdirs
+
+ # Add here commands to install the package into debian/ncoils.
+ cp ncoils $(CURDIR)/debian/ncoils/usr/bin/
+ cp *.mat $(CURDIR)/debian/ncoils/usr/share/ncoils/
+
+# Build architecture-independent files here.
+binary-indep: build install
+# We have nothing to do by default.
+
+# Build architecture-dependent files here.
+binary-arch: build install
+ dh_testdir
+ dh_testroot
+ dh_installchangelogs
+ dh_installdocs 1srya.fa *.pl
+ dh_installman debian/ncoils.1
+ dh_link
+ dh_strip
+ dh_compress
+ dh_fixperms
+ dh_installdeb
+ dh_shlibdeps
+ dh_gencontrol
+ dh_md5sums
+ dh_builddeb
+
+binary: binary-indep binary-arch
+.PHONY: build clean binary-indep binary-arch binary install configure
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