[med-svn] r3836 - in trunk/packages/theseus/trunk/debian: . patches
Andreas Tille
tille at alioth.debian.org
Mon Aug 31 10:57:50 UTC 2009
Author: tille
Date: 2009-08-31 10:57:50 +0000 (Mon, 31 Aug 2009)
New Revision: 3836
Added:
trunk/packages/theseus/trunk/debian/docs
trunk/packages/theseus/trunk/debian/examples
trunk/packages/theseus/trunk/debian/manpages
trunk/packages/theseus/trunk/debian/patches/00-makefile.patch
trunk/packages/theseus/trunk/debian/patches/10_kbsd.patch
trunk/packages/theseus/trunk/debian/patches/200-make.inc.patch
trunk/packages/theseus/trunk/debian/patches/99-theseus_align.sh.patch
trunk/packages/theseus/trunk/debian/patches/series
Removed:
trunk/packages/theseus/trunk/debian/patches/00-makefile.dpatch
trunk/packages/theseus/trunk/debian/patches/00list
trunk/packages/theseus/trunk/debian/patches/01-theseus.1.dpatch
trunk/packages/theseus/trunk/debian/patches/200-make.inc.dpatch
trunk/packages/theseus/trunk/debian/patches/99-theseus_align.sh.dpatch
trunk/packages/theseus/trunk/debian/theseus_align
Modified:
trunk/packages/theseus/trunk/debian/changelog
trunk/packages/theseus/trunk/debian/control
trunk/packages/theseus/trunk/debian/rules
Log:
Large chunk of changes concerning: Switch to quilt, use short debhelper 7 debian/rules file, use debian/{docs,manpages,examples}, do not tweak upstream tarball, added missing suggests
Modified: trunk/packages/theseus/trunk/debian/changelog
===================================================================
--- trunk/packages/theseus/trunk/debian/changelog 2009-08-30 11:42:01 UTC (rev 3835)
+++ trunk/packages/theseus/trunk/debian/changelog 2009-08-31 10:57:50 UTC (rev 3836)
@@ -7,6 +7,14 @@
- debhelper 7
- Build-Depends: libtool
- Standards-Version: 3.8.3 (no changes needed)
+ * Switched to quilt (affects debian/patches/*, debian/control,
+ debian/rules)
+ * Added Suggests: clustlaw, mafft, t-coffee, kalign, dialign
+ because these are called in theseus_align
+ * Use debian/{docs,manpages, examples} instead of arguments of
+ the debhelper installers to enable short rules file
+ * Reenabled patch for theseus_align and do not tweak upstream
+ tarball just to s?usr/local/bin?usr/bin?
-- Andreas Tille <tille at debian.org> Mon, 17 Aug 2009 15:50:19 +0200
Modified: trunk/packages/theseus/trunk/debian/control
===================================================================
--- trunk/packages/theseus/trunk/debian/control 2009-08-30 11:42:01 UTC (rev 3835)
+++ trunk/packages/theseus/trunk/debian/control 2009-08-31 10:57:50 UTC (rev 3836)
@@ -5,7 +5,7 @@
Uploaders: Morten Kjeldgaard <mok0 at ubuntu.com>,
Andreas Tille <tille at debian.org>
DM-Upload-Allowed: yes
-Build-Depends: debhelper (>= 7), dpatch, libgsl0-dev, liblapack-dev, libtool
+Build-Depends: debhelper (>= 7), quilt, libgsl0-dev, liblapack-dev, libtool
Standards-Version: 3.8.3
Homepage: http://www.theseus3d.org
Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/theseus/trunk/
@@ -14,7 +14,7 @@
Package: theseus
Architecture: any
Depends: ${shlibs:Depends}
-Suggests: muscle
+Suggests: muscle, clustlaw, mafft, t-coffee, kalign, dialign
Description: superimpose macromolecules using maximum likelihood
Theseus is a program that simultaneously superimposes multiple
macromolecular structures. Theseus finds the optimal solution to the
Added: trunk/packages/theseus/trunk/debian/docs
===================================================================
--- trunk/packages/theseus/trunk/debian/docs (rev 0)
+++ trunk/packages/theseus/trunk/debian/docs 2009-08-31 10:57:50 UTC (rev 3836)
@@ -0,0 +1 @@
+debian/citation.bib
Added: trunk/packages/theseus/trunk/debian/examples
===================================================================
--- trunk/packages/theseus/trunk/debian/examples (rev 0)
+++ trunk/packages/theseus/trunk/debian/examples 2009-08-31 10:57:50 UTC (rev 3836)
@@ -0,0 +1,2 @@
+examples/*
+debian/getexamples
Added: trunk/packages/theseus/trunk/debian/manpages
===================================================================
--- trunk/packages/theseus/trunk/debian/manpages (rev 0)
+++ trunk/packages/theseus/trunk/debian/manpages 2009-08-31 10:57:50 UTC (rev 3836)
@@ -0,0 +1,2 @@
+theseus.1
+debian/theseus_align.1
Deleted: trunk/packages/theseus/trunk/debian/patches/00-makefile.dpatch
===================================================================
--- trunk/packages/theseus/trunk/debian/patches/00-makefile.dpatch 2009-08-30 11:42:01 UTC (rev 3835)
+++ trunk/packages/theseus/trunk/debian/patches/00-makefile.dpatch 2009-08-31 10:57:50 UTC (rev 3836)
@@ -1,19 +0,0 @@
-#! /bin/sh /usr/share/dpatch/dpatch-run
-## 00makefile.dpatch by Morten Kjeldgaard <mok0 at ubuntu.com>
-##
-## All lines beginning with `## DP:' are a description of the patch.
-## DP: Use rm -f in clean target
-
- at DPATCH@
-diff -urNad theseus-1.3.4~/Makefile theseus-1.3.4/Makefile
---- theseus-1.3.4~/Makefile 2008-04-16 16:13:23.000000000 +0200
-+++ theseus-1.3.4/Makefile 2008-11-17 12:32:24.000000000 +0100
-@@ -145,6 +145,6 @@
- cp lib/*.a ${LOCALLIBDIR}
-
- clean:
-- find . -name '*.[oa]' -exec rm {} \;
-- rm theseus &> /dev/null
-+ find . -name '*.[oa]' -exec rm -f {} \;
-+ rm -f theseus &> /dev/null
-
Added: trunk/packages/theseus/trunk/debian/patches/00-makefile.patch
===================================================================
--- trunk/packages/theseus/trunk/debian/patches/00-makefile.patch (rev 0)
+++ trunk/packages/theseus/trunk/debian/patches/00-makefile.patch 2009-08-31 10:57:50 UTC (rev 3836)
@@ -0,0 +1,15 @@
+Fix clean target of original Makefile
+Author: Morten Kjeldgaard <mok0 at ubuntu.com>
+Switched to quilt: Andreas Tille <tille at debian.org>
+
+--- theseus-1.3.4~/Makefile 2008-04-16 16:13:23.000000000 +0200
++++ theseus-1.3.4/Makefile 2008-11-17 12:32:24.000000000 +0100
+@@ -145,6 +145,6 @@
+ cp lib/*.a ${LOCALLIBDIR}
+
+ clean:
+- find . -name '*.[oa]' -exec rm {} \;
+- rm theseus &> /dev/null
++ find . -name '*.[oa]' -exec rm -f {} \;
++ rm -f theseus &> /dev/null
+
Deleted: trunk/packages/theseus/trunk/debian/patches/00list
===================================================================
--- trunk/packages/theseus/trunk/debian/patches/00list 2009-08-30 11:42:01 UTC (rev 3835)
+++ trunk/packages/theseus/trunk/debian/patches/00list 2009-08-31 10:57:50 UTC (rev 3836)
@@ -1,2 +0,0 @@
-00-makefile.dpatch
-200-make.inc.dpatch
Deleted: trunk/packages/theseus/trunk/debian/patches/01-theseus.1.dpatch
===================================================================
--- trunk/packages/theseus/trunk/debian/patches/01-theseus.1.dpatch 2009-08-30 11:42:01 UTC (rev 3835)
+++ trunk/packages/theseus/trunk/debian/patches/01-theseus.1.dpatch 2009-08-31 10:57:50 UTC (rev 3836)
@@ -1,405 +0,0 @@
-#! /bin/sh /usr/share/dpatch/dpatch-run
-## 01-theseus.1.dpatch by Morten Kjeldgaard <mok0 at ubuntu.com>
-##
-## All lines beginning with `## DP:' are a description of the patch.
-## DP: Correct version number in manpage, and fix some hyphen issues.
-
- at DPATCH@
-diff -urNad theseus~/theseus.1 theseus/theseus.1
---- theseus~/theseus.1 2008-01-22 16:52:21.000000000 +0100
-+++ theseus/theseus.1 2008-11-17 13:21:36.000000000 +0100
-@@ -1,31 +1,31 @@
- .\" use 'man groff_man' to see the man page format macros
- .\" ----------------------------------------------------------------------------
--.TH THESEUS 1.2.6 "22 January 2008" "Brandeis University" "Likelihood Rocks"
-+.TH THESEUS 1 "22 January 2008" "Brandeis University" "Likelihood Rocks"
- .\" ----------------------------------------------------------------------------
- .SH NAME
- .\" ----
- .\"
- .B theseus
--v. 1.2.6 \- Maximum likelihood, multiple simultaneous superpositions
-+\- Maximum likelihood, multiple simultaneous superpositions
- with statistical analysis
- .\" ----------------------------------------------------------------------------
- .SH SYNOPSIS
- .\" --------
- .\"
- .B theseus
--[-aAbBcCdDeEfFgGhHiIjklLmMnNoOpPqQrRsStTuvVwWxXyYZ]
-+[\-aAbBcCdDeEfFgGhHiIjklLmMnNoOpPqQrRsStTuvVwWxXyYZ]
- .I pdbfile1 [pdbfile2 ...]
- .P
- and
- .P
- .B theseus_align
--[-aAbBcCdDeEfFgGhHiIjklLmMnNoOpPqQrRsStTuvVwWxXyYZ] -f
-+[\-aAbBcCdDeEfFgGhHiIjklLmMnNoOpPqQrRsStTuvVwWxXyYZ] \-f
- .I pdbfile1 [pdbfile2 ...]
- .P
- Default usage is equivalent to:
- .P
- .B theseus
---a0 -e2 -g1 -i200 -k-1 -p1e-7 -r theseus -v -P0
-+\-a0 \-e2 \-g1 \-i200 \-k-1 \-p1e-7 \-r theseus \-v \-P0
- .I your.pdb
- .\" ----------------------------------------------------------------------------
- .SH DESCRIPTION
-@@ -70,13 +70,13 @@
- different species or multiple mutated structures of hen egg white lysozyme.
- This mode requires the user to supply a sequence alignment file of the
- structures being superpositioned (see option
--.B "-A"
-+.B "\-A"
- and "FILE FORMATS" below).
- Additionally, it may be necessary to supply a mapfile that tells
- .B theseus
- which PDB structure files correspond to which sequences in the alignment (see
- option
--.B "-M"
-+.B "\-M"
- and "FILE FORMATS" below). When superpositioning based on a seqeunce
- alignment,
- .B theseus
-@@ -95,7 +95,7 @@
- Example 1:
- .IP
- .B theseus
---A cytc.aln -M cytc.filemap d1cih__.pdb d1csu__.pdb d1kyow_.pdb
-+\-A cytc.aln \-M cytc.filemap d1cih__.pdb d1csu__.pdb d1kyow_.pdb
- .IP
- In the above example,
- d1cih__.pdb, d1csu__.pdb, and d1kyow_.pdb
-@@ -104,7 +104,7 @@
- Example 2:
- .IP
- .B theseus_align
---f d1cih__.pdb d1csu__.pdb d1kyow_.pdb
-+\-f d1cih__.pdb d1csu__.pdb d1kyow_.pdb
- .IP
- In this example, the
- .B theseus_align
-@@ -129,7 +129,7 @@
-
- .TP
- .PD
--.BI "-a [" selection ]
-+.BI "\-a [" selection ]
- Atoms to include in the superposition.
- This option takes two types of arguments, either (1) a number specifying a
- preselected set of atom types, or (2) an explict PDB-style, colon-delimited list
-@@ -154,7 +154,7 @@
- .PD
- .IP
- Note, only the
--.B "-a0"
-+.B "\-a0"
- option is available when superpositioning structures with
- different sequences.
- .IP
-@@ -164,13 +164,13 @@
- Multiple atom types must be delimited by a colon.
- For example,
- .IP
--.B "-a' N : CA : C : O '
-+.B "\-a' N : CA : C : O '
- .IP
- would specify the atom types in the peptide backbone.
-
-
- .TP
--.B "-c"
-+.B "\-c"
- Use ML atomic covariance weighting (fit correlations, much slower)
- .IP
- Unless you have many different structures with few residues, fitting the
-@@ -178,7 +178,7 @@
- parameters and a paucity of data.
-
- .TP
--.BI "-e [" n ]
-+.BI "\-e [" n ]
- Embedding algorithm for initializing the average structure
- .PD 0
- .RS 8
-@@ -190,11 +190,11 @@
- .PD
-
- .TP
--.BI "-f"
-+.BI "\-f"
- Only read the first model of a multi-model PDB file
-
- .TP
--.BI "-g [" n ]
-+.BI "\-g [" n ]
- Hierarchical model for variances
- .PD 0
- .RS 8
-@@ -206,33 +206,33 @@
- .PD
-
- .TP
--.B "-h"
-+.B "\-h"
- Help/usage
-
- .TP
--.BI "-i [" nnn ]
-+.BI "\-i [" nnn ]
- Maximum iterations, {200}
-
- .TP
--.BI "-k [" n ]
--constant minimum variance {-1}
-+.BI "\-k [" n ]
-+constant minimum variance {\-1}
- {if set to negative value, the minimum variance is determined empirically}
-
- .TP
--.BI "-p [" precision ]
--Requested relative precision for convergence, {1e-7}
-+.BI "\-p [" precision ]
-+Requested relative precision for convergence, {1e\-7}
-
- .TP
--.BI "-r [" "root name" ]
-+.BI "\-r [" "root name" ]
- Root name to be used in naming the output files, {theseus}
-
- .TP
--.BI "-s [" n-n:... ]
--Residue selection (e.g. -s15-45:50-55), {all}
-+.BI "\-s [" n\-n:... ]
-+Residue selection (e.g. \-s15\-45:50\-55), {all}
-
- .TP
--.BI "-S [" n-n:... ]
--Residues to exclude (e.g. -S15-45:50-55) {none}
-+.BI "\-S [" n\-n:... ]
-+Residues to exclude (e.g. \-S15-\45:50\-55) {none}
- .IP
- The previous two options have the same format. Residue (or alignment column)
- ranges are indicated by beginning and end separated by a dash.
-@@ -240,31 +240,31 @@
- Chains may also be selected by giving the chain ID immediately preceding the
- residue range.
- For example,
--.B -sA1-20:A40-71
-+.B \-sA1\-20:A40\-71
- will only include residues 1 through 20
- and 40 through 70 in chain A. Chains cannot be specified when superpositioning
- structures with different sequences.
-
- .TP
--.B "-v"
-+.B "\-v"
- use ML variance weighting (no correlations) {default}
-
- .PD
- .SS Input/output options:
-
- .TP
--.BI "-A [" "sequence alignment file" ]
-+.BI "\-A [" "sequence alignment file" ]
- Sequence alignment file to use as a guide (CLUSTAL or A2M format)
- .IP
- For use when superpositioning structures with different sequences.
- See "FILE FORMATS" below.
-
- .TP
--.B "-E"
-+.B "\-E"
- Print expert options
-
- .TP
--.B "-F"
-+.B "\-F"
- Print FASTA files of the sequences in PDB files and quit
- .IP
- A useful option when superpositioning structures with different sequences.
-@@ -273,39 +273,39 @@
- alignment file used as
- .B theseus
- input with the
--.B "-A"
-+.B "\-A"
- option.
-
- .TP
--.B "-h"
-+.B "\-h"
- Help/usage
-
- .TP
--.B "-I"
-+.B "\-I"
- Just calculate statistics for input file; don't superposition
-
- .TP
--.BI "-M [" mapfile ]
-+.BI "\-M [" mapfile ]
- File that maps sequences in the alignment file to PDB files
- .IP
- A simple two-column formatted file; see "FILE FORMATS" below. Used with mode 2.
-
- .TP
--.B "-n"
-+.B "\-n"
- Don't write transformed pdb file
-
- .TP
--.BI "-o [" "reference structure" ]
-+.BI "\-o [" "reference structure" ]
- Reference file to superposition on, all rotations are relative to the first
- model in this file
- .IP
--For example, 'theseus -o cytc1.pdb cytc1.pdb cytc2.pdb cytc3.pdb' will
-+For example, 'theseus \-o cytc1.pdb cytc1.pdb cytc2.pdb cytc3.pdb' will
- superposition the structures and rotate the entire final superposition so that
- the structure from cytc1.pdb is in the same orientation as the structure in the
- original cytc1.pdb PDB file.
-
- .TP
--.B "-O"
-+.B "\-O"
- Olve's segID file
- .IP
- Useful output when superpositioning structures with different sequences (mode 2).
-@@ -321,26 +321,26 @@
- the very atoms that were included in the ML superposition calculation.
- That is, it will only contain alpha carbons or phosphorous atoms, and it will
- only contain atoms from the columns selected with the
--.B "-s"
-+.B "\-s"
- or
- .B
--"-S"
-+"\-S"
- options.
- Requested by Olve Peersen of Colorado State University.
-
- .TP
--.B "-V"
-+.B "\-V"
- Version
-
- .PD
- .SS Principal components analysis:
-
- .TP
--.B "-C"
-+.B "\-C"
- Use covariance matrix for PCA (correlation matrix is default)
-
- .TP
--.BI "-P [" nnn ]
-+.BI "\-P [" nnn ]
- Number of principal components to calculate {0}
-
- .IP
-@@ -358,23 +358,23 @@
-
- .P
- .B theseus
---l -r new2sdf
-+\-l \-r new2sdf
- .I 2sdf.pdb
-
- .P
- .B theseus
---s15-45 -P3
-+\-s15\-45 \-P3
- .I 2sdf.pdb
-
- .P
- .B theseus
---A
-+\-A
- .I cytc.aln
---M
-+\-M
- .I cytc.mapfile
---o
-+\-o
- .I cytc1.pdb
---s1-40
-+\-s1\-40
- .I cytc1.pdb cytc2.pdb cytc3.pdb cytc4.pdb
- .\" ----------------------------------------------------------------------------
- .SH ENVIRONMENT
-@@ -408,7 +408,7 @@
- equal), a sequence alignment file must be included for
- .B theseus
- to use as a guide (specified by the
--.B "-A"
-+.B "\-A"
- option).
- .B Theseus
- accepts both CLUSTAL and A2M (FASTA) formatted multiple sequence alignment
-@@ -422,14 +422,14 @@
- PDB file. An easy way to ensure that your sequences exactly match the PDB
- files is to generate the sequences using
- .B theseus'
--.B "-F"
-+.B "\-F"
- option, which writes out a FASTA formatted sequence file of the chain(s)
- in the PDB files. The files output with this option can then be aligned with
- a multiple sequence alignment program such as CLUSTAL or MUSCLE, and the
- resulting output alignment file used as
- .B theseus
- input with the
--.B "-A"
-+.B "\-A"
- option.
-
- .PD
-@@ -439,7 +439,7 @@
- PDB file. That is, there can be extra sequences in the alignment that are
- not used for guiding the superposition.
-
--.SS PDB -> Sequence mapfile
-+.SS PDB \-> Sequence mapfile
-
- If the names of the PDB files and the names of the corresponding sequences
- in the alignemnt are identical, the mapfile may be omitted. Otherwise,
-@@ -447,7 +447,7 @@
- needs to know which sequences in the alignment file correspond to which
- PDB structure files. This information is included in a mapfile with a very
- simple format (specified with the
--.B "-M"
-+.B "\-M"
- option). There are only two columns separated by whitespace: the first column
- lists the names of the PDB structure files, while the second column lists the
- corresponding sequence names exactly as given in the multiple sequence
-@@ -526,10 +526,10 @@
- model is a matrix Gaussian distribution of the structures with equal
- variances and no correlations. For the ML fits, the assumed models can
- either be (1) unequal variances and no correlations, as calculated with the
--.B "-v"
-+.B "\-v"
- option [default] or (2) unequal variances and correlations, as calculated
- with the
--.B "-c"
-+.B "\-c"
- option. This statistic is for the superposition only, and does
- not include the fit of the covariance matrix eigenvalues to an inverse gamma
- distribution. See 'Omnibus chi^2' below.
-@@ -641,7 +641,7 @@
- .PD
- .P
- When Principal Components are calculated (with the
--.B "-P"
-+.B "\-P"
- option), the following
- files are also produced:
-
-@@ -738,7 +738,7 @@
- PLOS Computational Biology,
- .I in press
-
--.\" ----------------------------------------------------------------------------
-+.\" ---------------------------------------------------------------------------
- .SH HISTORY
- .\" -------
- .\"
Added: trunk/packages/theseus/trunk/debian/patches/10_kbsd.patch
===================================================================
--- trunk/packages/theseus/trunk/debian/patches/10_kbsd.patch (rev 0)
+++ trunk/packages/theseus/trunk/debian/patches/10_kbsd.patch 2009-08-31 10:57:50 UTC (rev 3836)
@@ -0,0 +1,35 @@
+Purpose: Enable Building on kbsd architecture
+Author: Cyril Brulebois <kibi at debian.org>, Andreas Tille <tille at debian.org>
+Fixes: #542879
+
+--- theseus.orig/distfit.h
++++ theseus/distfit.h
+@@ -713,7 +713,7 @@
+ #ifndef LOGNORMAL_SEEN
+ #define LOGNORMAL_SEEN
+
+-#ifdef __linux__
++#ifdef __linux__ || defined(__GLIBC__)
+ extern double erf(double x);
+ #endif
+
+@@ -1446,7 +1446,7 @@
+ #ifndef VONMISES_DIST_SEEN
+ #define VONMISES_DIST_SEEN
+
+-#ifdef __linux__
++#ifdef __linux__ || defined(__GLIBC__)
+ extern double jn(int n, double x);
+ #endif
+
+--- theseus.orig/theseus.h
++++ theseus/theseus.h
+@@ -51,7 +51,7 @@
+ #include <string.h>
+ #include <stdio.h>
+ #include <unistd.h>
+-#ifdef __linux__
++#ifdef __linux__ || defined(__GLIBC__)
+ #include <getopt.h>
+ #endif
+ #include <ctype.h>
Deleted: trunk/packages/theseus/trunk/debian/patches/200-make.inc.dpatch
===================================================================
--- trunk/packages/theseus/trunk/debian/patches/200-make.inc.dpatch 2009-08-30 11:42:01 UTC (rev 3835)
+++ trunk/packages/theseus/trunk/debian/patches/200-make.inc.dpatch 2009-08-31 10:57:50 UTC (rev 3836)
@@ -1,27 +0,0 @@
-#! /bin/sh /usr/share/dpatch/dpatch-run
-## 200-makefile.dpatch by Morten Kjeldgaard <mok at bioxray.dk>
-##
-## All lines beginning with `## DP:' are a description of the patch.
-## DP: Customize make.inc for Ubuntu building
-
- at DPATCH@
-diff -urNad theseus-1.3.4~/make.inc theseus-1.3.4/make.inc
---- theseus-1.3.4~/make.inc 2008-11-17 12:52:53.000000000 +0100
-+++ theseus-1.3.4/make.inc 2008-11-17 12:53:04.000000000 +0100
-@@ -195,3 +195,16 @@
- # CFLAGS = $(WARN)
- # CC = cc
-
-+
-+# Ubuntu Linux x86 & amd64
-+SYSLIBS = -lpthread -lm -lc
-+LIBS = -Llib -ldistfit -lgsl -lmsa -ldssplite -ldltmath -lDLTutils
-+BLASLIB = -L/usr/lib/atlas -llapack
-+BLASLIBDIR =
-+LAPACKLIB =
-+LAPACKLIBDIR =
-+INSTALLDIR =
-+OPT = -g -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -ftree-vectorize
-+WARN = -Wall -pedantic -std=c99
-+CFLAGS += $(WARN)
-+CC = gcc
Added: trunk/packages/theseus/trunk/debian/patches/200-make.inc.patch
===================================================================
--- trunk/packages/theseus/trunk/debian/patches/200-make.inc.patch (rev 0)
+++ trunk/packages/theseus/trunk/debian/patches/200-make.inc.patch 2009-08-31 10:57:50 UTC (rev 3836)
@@ -0,0 +1,23 @@
+Add Ububtu specific build options which work for Debian as well
+Author: Morten Kjeldgaard <mok at bioxray.dk>
+Switched to quilt: Andreas Tille <tille at debian.org>
+
+--- theseus-1.3.4~/make.inc 2008-11-17 12:52:53.000000000 +0100
++++ theseus-1.3.4/make.inc 2008-11-17 12:53:04.000000000 +0100
+@@ -195,3 +195,16 @@
+ # CFLAGS = $(WARN)
+ # CC = cc
+
++
++# Ubuntu Linux x86 & amd64
++SYSLIBS = -lpthread -lm -lc
++LIBS = -Llib -ldistfit -lgsl -lmsa -ldssplite -ldltmath -lDLTutils
++BLASLIB = -L/usr/lib/atlas -llapack
++BLASLIBDIR =
++LAPACKLIB =
++LAPACKLIBDIR =
++INSTALLDIR =
++OPT = -g -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -ftree-vectorize
++WARN = -Wall -pedantic -std=c99
++CFLAGS += $(WARN)
++CC = gcc
Deleted: trunk/packages/theseus/trunk/debian/patches/99-theseus_align.sh.dpatch
===================================================================
--- trunk/packages/theseus/trunk/debian/patches/99-theseus_align.sh.dpatch 2009-08-30 11:42:01 UTC (rev 3835)
+++ trunk/packages/theseus/trunk/debian/patches/99-theseus_align.sh.dpatch 2009-08-31 10:57:50 UTC (rev 3836)
@@ -1,26 +0,0 @@
-#! /bin/sh /usr/share/dpatch/dpatch-run
-## 99-theseus_align.sh.dpatch by <mok at bioxray.dk>
-##
-## All lines beginning with `## DP:' are a description of the patch.
-## DP: Define clustalw to be the active alignment program.
-## DP: Fix the directory where theseus is found -> /usr/bin.
-
- at DPATCH@
---- theseus_align.orig 2007-09-27 15:12:04.000000000 +0200
-+++ foo/theseus_align 2007-09-27 15:13:14.000000000 +0200
-@@ -41,13 +41,13 @@
- # The following six constant strings should be modified to whatever is
- # convenient and applicable.
-
--theseus="/usr/local/bin/theseus"; # where to find the THESEUS binary executable
-+theseus="/usr/bin/theseus"; # where to find the THESEUS binary executable
- fastafile="theseus.fasta";
- filemapfile="theseus.filemap";
- alignmentfile="theseus.aln";
-
- # for MUSCLE -- http://www.drive5.com/muscle/
--alignprog="/usr/local/bin/muscle";
-+alignprog="/usr/bin/muscle";
- align_cmd="${alignprog} -maxiters 32 -in ${fastafile} -out ${alignmentfile} -clwstrict";
-
- # for CLUSTALW -- ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalW/
Added: trunk/packages/theseus/trunk/debian/patches/99-theseus_align.sh.patch
===================================================================
--- trunk/packages/theseus/trunk/debian/patches/99-theseus_align.sh.patch (rev 0)
+++ trunk/packages/theseus/trunk/debian/patches/99-theseus_align.sh.patch 2009-08-31 10:57:50 UTC (rev 3836)
@@ -0,0 +1,47 @@
+Fix path names in shell script to adapt to Debian locations of files
+ANTENTION: This patch is currently not used
+Authors: Morten Kjeldgaard <mok at bioxray.dk>, Andreas Tille <tille at debian.org>
+
+--- theseus.orig/theseus_align
++++ theseus/theseus_align
+@@ -41,33 +41,33 @@
+ # The following six constant strings should be modified to whatever is
+ # convenient and applicable.
+
+-theseus="/usr/local/bin/theseus"; # where to find the THESEUS binary executable
++theseus="/usr/bin/theseus"; # where to find the THESEUS binary executable
+ fastafile="theseus.fasta";
+ filemapfile="theseus.filemap";
+ alignmentfile="theseus.aln";
+
+ # for MUSCLE -- http://www.drive5.com/muscle/
+-alignprog="/usr/local/bin/muscle";
++alignprog="/usr/bin/muscle";
+ align_cmd="${alignprog} -maxiters 32 -in ${fastafile} -out ${alignmentfile} -clwstrict";
+
+ # for CLUSTALW -- ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalW/
+-#alignprog="/usr/local/bin/clustlaw";
++#alignprog="/usr/bin/clustlaw";
+ #align_cmd="${alignprog} -infile=${fastafile} -outfile=${alignmentfile}";
+
+ # for MAFFT -- http://www.biophys.kyoto-u.ac.jp/%7Ekatoh/programs/align/mafft/
+-#alignprog="/usr/local/bin/mafft";
++#alignprog="/usr/bin/mafft";
+ #align_cmd="${alignprog} --maxiterate 1000 --localpair --clustalout ${fastafile} > ${alignmentfile}";
+
+ # for T_COFFEE -- http://igs-server.cnrs-mrs.fr/%7Ecnotred/Projects_home_page/t_coffee_home_page.html
+-#alignprog="/usr/local/bin/t_coffee";
++#alignprog="/usr/bin/t_coffee";
+ #align_cmd="${alignprog} ${fastafile} -outfile=${alignmentfile}";
+
+ # for KALIGN -- http://msa.cgb.ki.se/
+-#alignprog="/usr/local/bin/kalign"
++#alignprog="/usr/bin/kalign"
+ #align_cmd="${alignprog} -i ${fastafile} -f aln | sed 's/Kalign/CLUSTALW/' > ${alignmentfile}";
+
+ # for DIALIGN2 -- http://bibiserv.techfak.uni-bielefeld.de/dialign/
+-#alignprog="/usr/local/bin/dialign2"
++#alignprog="/usr/bin/dialign2"
+ #align_cmd="${alignprog} -cw ${fastafile}; sed 's/\/\///' ${fastafile%.*}.cw | sed 's/DIALIGN/CLUSTALW/'";
+
+
Added: trunk/packages/theseus/trunk/debian/patches/series
===================================================================
--- trunk/packages/theseus/trunk/debian/patches/series (rev 0)
+++ trunk/packages/theseus/trunk/debian/patches/series 2009-08-31 10:57:50 UTC (rev 3836)
@@ -0,0 +1,4 @@
+00-makefile.patch
+200-make.inc.patch
+99-theseus_align.sh.patch
+10_kbsd.patch
Modified: trunk/packages/theseus/trunk/debian/rules
===================================================================
--- trunk/packages/theseus/trunk/debian/rules 2009-08-30 11:42:01 UTC (rev 3835)
+++ trunk/packages/theseus/trunk/debian/rules 2009-08-31 10:57:50 UTC (rev 3836)
@@ -1,64 +1,11 @@
#!/usr/bin/make -f
-# -*- mode: makefile; mode: font-lock -*-
+# rules file using dh for theseus
+# Copyright (C) Andreas Tille <tille at debian.org>
+# License: GPL
-include /usr/share/dpatch/dpatch.make
+%:
+ dh --with quilt $@
-# extract the upstream version from debian/changelog
-uvers := $(shell sed 's/.*(\(.*\)-.*).*/\1/;q' < debian/changelog)
-
-# Get the auxilliary script distributed separately
-get-orig-source:
- dh_testdir
- wget -q http://www.theseus3d.org/src/theseus_align \
- -O - | sed 's!/usr/local/bin!/usr/bin!' > debian/theseus_align
-build: patch-stamp build-stamp
-
-build-stamp:
- dh_testdir
-
- # compiler flags are hardwired in make.inc
- $(MAKE)
-
- touch $@
-
-clean: patch-stamp cleanfirst unpatch
-
-cleanfirst:
- dh_testdir
- dh_testroot
- rm -f build-stamp
-
- $(MAKE) clean
- rm -f theseus distfit
- dh_clean
-
-install: build
- dh_testdir
- dh_testroot
- dh_clean -k
-
-binary-indep: build install
-# Nothing to build here
-
-binary-arch: build install
- dh_testdir
- dh_testroot
- dh_install
- dh_installdocs debian/citation.bib
- dh_installchangelogs
- dh_installman theseus.1 debian/theseus_align.1
- dh_installexamples examples/* debian/getexamples
- dh_strip
- dh_compress
- dh_fixperms
- dh_installdeb
- dh_shlibdeps
- dh_gencontrol
- dh_md5sums
- dh_builddeb
-
-binary: binary-indep binary-arch
-
-.PHONY: build clean cleanfirst binary-indep binary-arch binary install get-orig-source
-
-####
+override_dh_auto_clean:
+ dh_quilt_patch
+ dh_auto_clean
Deleted: trunk/packages/theseus/trunk/debian/theseus_align
===================================================================
--- trunk/packages/theseus/trunk/debian/theseus_align 2009-08-30 11:42:01 UTC (rev 3835)
+++ trunk/packages/theseus/trunk/debian/theseus_align 2009-08-31 10:57:50 UTC (rev 3836)
@@ -1,204 +0,0 @@
-#!/bin/bash
-# THESEUS: Maximum likelihood superpositioning of multiple
-# macromolecular structures
-#
-# -/_|:|_|_\-
-# Douglas L. Theobald
-# Department of Biochemistry
-# Brandeis University
-# Waltham, MA 02454
-#
-# dtheobald at brandeis.edu
-# dtheobald at gmail.com
-#
-# theseus_align
-#
-# Usage: theseus_align [theseus_options] -f pdbfile1.pdb pdbfile2.pdb ...
-#
-# 'theseus_align' allows for a quick-and-dirty way to ML superposition proteins
-# with different sequences. It should work very well when the protein sequences
-# are relatively similar, although the ML method will still give much better
-# results than least-squares when the sequences are moderately divergent.
-# Technically, this procedure gives a structure-based superposition of a
-# sequence-based alignment. It _does not_ perform a structure-based alignment.
-#
-# First, the script uses THESEUS to create FASTA formatted sequence files
-# corresponding to the exact protein sequences found in the pdb files that you
-# supply.
-#
-# Second, these sequences are aligned using the multiple sequence alignment
-# program of your choice -- currently set up for MUSCLE and easily modified for
-# CLUSTALW, T_COFFEE, KALIGN, DIALIGN2, or MAFFT. Any multiple sequence
-# alignment program can be used, as long as it can generate clustal-formatted
-# files. However, I highly recommend Bob Edgar's MUSCLE program for both its
-# speed and accuracy. It is easy to install using either precompiled binaries or
-# by compiling from scratch:
-# http://www.drive5.com/muscle/
-#
-# Third, THESEUS performs a superposition of the structures using the sequence
-# alignment as a guide.
-#
-# The following six constant strings should be modified to whatever is
-# convenient and applicable.
-
-theseus="/usr/bin/theseus"; # where to find the THESEUS binary executable
-fastafile="theseus.fasta";
-filemapfile="theseus.filemap";
-alignmentfile="theseus.aln";
-
-# for MUSCLE -- http://www.drive5.com/muscle/
-alignprog="/usr/bin/muscle";
-align_cmd="${alignprog} -maxiters 32 -in ${fastafile} -out ${alignmentfile} -clwstrict";
-
-# for CLUSTALW -- ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalW/
-#alignprog="/usr/bin/clustlaw";
-#align_cmd="${alignprog} -infile=${fastafile} -outfile=${alignmentfile}";
-
-# for MAFFT -- http://www.biophys.kyoto-u.ac.jp/%7Ekatoh/programs/align/mafft/
-#alignprog="/usr/bin/mafft";
-#align_cmd="${alignprog} --maxiterate 1000 --localpair --clustalout ${fastafile} > ${alignmentfile}";
-
-# for T_COFFEE -- http://igs-server.cnrs-mrs.fr/%7Ecnotred/Projects_home_page/t_coffee_home_page.html
-#alignprog="/usr/bin/t_coffee";
-#align_cmd="${alignprog} ${fastafile} -outfile=${alignmentfile}";
-
-# for KALIGN -- http://msa.cgb.ki.se/
-#alignprog="/usr/bin/kalign"
-#align_cmd="${alignprog} -i ${fastafile} -f aln | sed 's/Kalign/CLUSTALW/' > ${alignmentfile}";
-
-# for DIALIGN2 -- http://bibiserv.techfak.uni-bielefeld.de/dialign/
-#alignprog="/usr/bin/dialign2"
-#align_cmd="${alignprog} -cw ${fastafile}; sed 's/\/\///' ${fastafile%.*}.cw | sed 's/DIALIGN/CLUSTALW/'";
-
-
-################################################################################
-################################################################################
-# NOTHING BELOW HERE SHOULD BE CHANGED
-################################################################################
-
-if [ ! -f ${alignprog} ] || [ ! -x ${alignprog} ] || [ ! -s ${alignprog} ]
-then
- printf "\nERROR: Problem with multiple sequence aligment executable, ${alignprog}\n";
- ${alignprog};
- exit 1;
-elif [ ! -f ${theseus} ] || [ ! -x ${theseus} ] || [ ! -s ${theseus} ]
-then
- printf "\nERROR: Problem with THESEUS executable, ${alignprog}\n";
- ${theseus};
- exit 1;
-fi
-
-usage="Usage: ${0} [theseus_options] -f pdbfile1.pdb pdbfile2.pdb ...";
-
-declare -a opts=( $@ ); # save the command line arguments
-(( argc = $# )); # save the number of command line arguments
-
-# shift up until we get past '-f', which signifies that the rest are files
-(( optn = 0 ));
-while [ "${1}" != "-f" ] && [ ! -z "${1}" ]
-do
- shift;
- (( optn++ ));
-done
-
-# Ensure that there is something on the command line
-if [[ -z "$@" ]] # double brackets don't do word splitting
-then
- printf "\n${usage}\n\n";
- exit 1;
-else
- shift;
-fi
-
-for (( i = optn; i < argc; ++i ))
-do
- unset opts[${i}]; # nix the pdb files from the options array
-done
-
-pdbs="$@";
-echo ${pdbs}
-
-# Make sure there are pdb files on the command line
-if [[ -z "${pdbs}" ]] # double brackets don't do word splitting
-then
- printf "\n${usage}\n\n";
- exit 1;
-else
- shift;
-fi
-
-# Check each pdb file to see if it exists, if it is readable, and if it is non-empty
-for pdb in ${pdbs}
-do
- if [ ! -f ${pdb} ] || [ ! -r ${pdb} ] || [ ! -s ${pdb} ]
- then
- printf "\nProblem with file: ${pdb}\n"
- printf "\n${usage}\n\n";
- exit 1;
- fi
-done
-
-theseus_cmd="${theseus} ${opts[@]} -f -M ${filemapfile} -A ${alignmentfile} ${pdbs}";
-
-# Use THESEUS to make fasta sequence files corresponding to each pdb
-${theseus} -f -F ${pdbs};
-
-if [ ! $? ]
-then
- printf "\nERROR: THESEUS did not successfully create all FASTA sequence files.\n";
- printf "\n${usage}\n\n";
- exit 1;
-fi
-
-for pdb in ${pdbs}
-do
- fasta="${pdb}.fst";
- if [ ! -f ${fasta} ] || [ ! -r ${fasta} ] || [ ! -s ${fasta} ]
- then
- printf "\nProblem with FASTA sequence file ${fastafile} for ${pdb}\n"
- printf "\n${usage}\n\n";
- exit 1;
- fi
-done
-
-if [ -f ${fastafile} ]
-then
- rm ${fastafile};
-fi
-
-# Concatenate all fasta files into one large multiple sequence fasta file
-for pdb in ${pdbs}
-do
- cat ${pdb}.fst >> ${fastafile};
-done
-
-#ls -1 ${pdbs} | awk '{print $1" "$1}' > ${filemapfile};
-
-if [ -f ${filemapfile} ]
-then
- rm ${filemapfile};
-fi
-
-# Make the mapfile for THESEUS to use (which sequence corresponds to which file)
-for pdb in ${pdbs}
-do
- echo "${pdb} ${pdb}" >> ${filemapfile};
-done
-
-# Align the sequences
-printf "\n\n${align_cmd}\n";
-${align_cmd};
-
-if [ ! $? ]
-then
- printf "\nERROR: Sequence alignment failed.\n";
- printf "\n${usage}\n\n";
- exit 1;
-fi
-
-# Superimpose with THESEUS based on the sequence alignment generated above
-printf "\n\n${theseus_cmd}\n";
-${theseus_cmd};
-
-exit 0;
-
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