--- theseus-1.4.3.orig/debian/changelog +++ theseus-1.4.3/debian/changelog @@ -0,0 +1,80 @@ +theseus (1.4.3-2) unstable; urgency=low + + * debian/patches/10_kbsd.patch: Correctly applied patch from + Cyril (sorry for mixing this up) + Closes: #542879 + + -- Andreas Tille Thu, 03 Sep 2009 08:49:22 +0200 + +theseus (1.4.3-1) unstable; urgency=low + + [Andreas Tille] + * New upstream version + Closes: #534630 + * debian/control + - Added myself to uploaders + - 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 + * Re-enabled patch for theseus_align and do not tweak upstream + tarball just to s?usr/local/bin?usr/bin? + * debian/patches/200-make.inc.patch: Use ar directly to to avoid + problems with libtool, drop -arch command line options to gcc + which let compilation fail + * debian/README.Debian: Removed paragraph about theseus_align + because this is now shipped in upstream tarball + * debian/patches/10_kbsd.patch: fix the FTBFS problem reported by + Cyril Brulebois (thanks to Cyril for the patch) + Closes: #542879 + + [Morten Kjeldgaard] + * Fix FTBFS on certain platforms that lack the Atlas libraries + by using lapack-dev in Build-Depends. This will pull in Atlas + on the relevant platforms, otherwise not. + + -- Andreas Tille Mon, 31 Aug 2009 14:50:19 +0200 + +theseus (1.3.9-1) unstable; urgency=low + + * New upstream release, first upload to Debian. + + -- Morten Kjeldgaard Sun, 16 Nov 2008 22:36:36 +0100 + +theseus (1.1.5-0ubuntu3) intrepid; urgency=low + + * gfortran transition for intrepid, atlas3-base -> libatlas3-base. + + -- Morten Kjeldgaard Thu, 04 Sep 2008 23:20:52 +0200 + +theseus (1.1.5-0ubuntu2) hardy; urgency=low + + * debian/rules: FTBFS on all archs but i386, due to missing + binary-arch target (LP: #181359) + * Removed redundant libraries. + + -- Morten Kjeldgaard Tue, 08 Jan 2008 22:35:42 +0100 + +theseus (1.1.5-0ubuntu1) hardy; urgency=low + + * Initial release (LP: #173506) + * The upstream tarball has been versioned as 1.1.5 (not versioned upstream) + The get-orig-source target in debian/rules can be used for this purpose + once the changelog has been edited to contain the right version + * Patch to theseus.1 and theseus_align.1 + - fix incorrect .TH line in theseus.1 + - fix multiple instances of hyphen (-) to minus (\-) + * Patch on thesus_align.sh. The script is patched to find + programs in /usr/bin. The script makes use of the + multiple sequence alignment program muscle, which is available + from universe. + * Patch make.inc to provide correct compiler switches. + * A script (getexamples) is provided to show the user how (s)he can + download the data in examples/ + + -- Morten Kjeldgaard Sun, 02 Dec 2007 15:53:15 +0100 --- theseus-1.4.3.orig/debian/citation.bib +++ theseus-1.4.3/debian/citation.bib @@ -0,0 +1,43 @@ +@article{Douglas L.Theobald12052006, +author = {Theobald, Douglas L. and Wuttke, Deborah S.}, +title={{Empirical Bayes hierarchical models for regularizing maximum likelihood estimation in the matrix Gaussian Procrustes problem}}, +journal = {Proceedings of the National Academy of Sciences}, +volume = {103}, +number = {49}, +pages = {18521-18527}, +doi = {10.1073/pnas.0508445103}, +year = {2006}, +URL = {http://www.pnas.org/content/103/49/18521.abstract}, +eprint = {http://www.pnas.org/content/103/49/18521.full.pdf+html} +} + +@article{DouglasL. Theobald09012006, +author = {Theobald, Douglas L. and Wuttke, Deborah S.}, +title = {{THESEUS: maximum likelihood superpositioning and analysis of macromolecular structures}}, +journal = {Bioinformatics}, +volume = {22}, +number = {17}, +pages = {2171-2172}, +doi = {10.1093/bioinformatics/btl332}, +year = {2006}, +URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/17/2171}, +eprint = {http://bioinformatics.oxfordjournals.org/cgi/reprint/22/17/2171.pdf} +} + +@article{10.1371/journal.pcbi.0040043, + author = {Theobald, Douglas L AND Wuttke, Deborah S}, + journal = {PLoS Comput Biol}, + publisher = {Public Library of Science}, + title = {Accurate Structural Correlations from Maximum Likelihood Superpositions}, + year = {2008}, + month = {Feb}, + volume = {4}, + url = {http://dx.doi.org/10.1371%2Fjournal.pcbi.0040043}, + pages = {e43}, + number = {2}, + doi = {10.1371/journal.pcbi.0040043} +} + + + + --- theseus-1.4.3.orig/debian/compat +++ theseus-1.4.3/debian/compat @@ -0,0 +1 @@ +7 --- theseus-1.4.3.orig/debian/control +++ theseus-1.4.3/debian/control @@ -0,0 +1,29 @@ +Source: theseus +Section: science +Priority: optional +Maintainer: Debian Med Packaging Team +Uploaders: Morten Kjeldgaard , + Andreas Tille +DM-Upload-Allowed: yes +Build-Depends: debhelper (>= 7.1), 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/ +Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/theseus/trunk/?rev=0&sc=0 + +Package: theseus +Architecture: any +Depends: ${shlibs:Depends}, ${misc:Depends} +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 + superposition problem using the method of maximum likelihood. By + down-weighting variable regions of the superposition and by correcting for + correlations among atoms, the ML superposition method produces very + accurate structural alignments. + . + When macromolecules with different residue sequences are superimposed, + other programs and algorithms discard residues that are aligned with + gaps. Theseus, however, uses a novel superimposition algorithm that + includes all of the data. --- theseus-1.4.3.orig/debian/copyright +++ theseus-1.4.3/debian/copyright @@ -0,0 +1,86 @@ +Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat?action=recall&rev=196 +Upstream-Name: Theseus +Upstream-Maintainer: Douglas Theobald +Upstream-Source: http://www.theseus3d.org/src/theseus.tar.gz + +Files: * +Copyright: © 2003-2007, Douglas L. Theobald +License: GPL-2+ + THESEUS 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 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., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA + +X-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'. + + +Files: lbidltmath/ncbi_math.* +Copyright: © 1991, Gish, Kans, Ostell and Schuler +License: GPL-2+ + + +Files: libdltmath/myrandom.c +Copyright: © 2002, Takuji Nishimura and Makoto Matsumoto +License: GPL-2+ + + +Files: examples/* +Copyright: PD +License: + ADVISORY NOTICE FOR USE OF THE PDB ARCHIVE + . + By using the materials available in this archive, the user agrees to abide + by the following conditions: + . + * The archival data files in the PDB archive are made freely available + to all users. Data files within the archive may be redistributed in original + form without restriction. Redistribution of modified data files using the same + file name as is on the FTP server is prohibited. The rules for file names are + detailed at http://www.wwpdb.org/wwpdb_charter.html. + . + * Data files containing PDB content may incorporate the PDB 4-letter entry + name (e.g. 1ABC) in standard PDB records only if they are exactly the same + as what is residing in the PDB archive. This does not prevent databases + from including PDB entry_id's as cross-references where it is clear that + they refer to the PDB archive. PDB records refer to the standard PDB format. + The distribution of modified PDB format data including the records: HEADER, + CAVEAT, REVDAT, SPRSDE, DBREF, SEQADV, and MODRES are not allowed. + . + * The user assumes all responsibility for insuring that intellectual property + claims associated with any data set deposited in the PDB archive are honored. + It should be understood that the PDB data files do not contain any information + on intellectual property claims with the exception in some cases of a reference + for a patent involving the structure. + . + * Any opinion, findings, and conclusions expressed in the PDB archive by the + authors/contributors do not necessarily reflect the views of the wwPDB. + . + * The data in the PDB archive are provided on an "as is" basis. The wwPDB + nor its comprising institutions cannot be held liable to any party for direct, + indirect, special, incidental, or consequential damages, including lost + profits, arising from the use of PDB materials. + . + * Resources on this site are provided without warranty of any kind, either + expressed or implied. This includes but is not limited to merchantability or + fitness for a particular purpose. The institutions managing this site make + no representation that these resources will not infringe any patent or other + proprietary right. + +X-Comment: The files in examples/ are in the public domain, and can be copied + and distributed with no restriction. It is scientific data from the Protein + Data Bank (http://www.pdb.org) and the database ASTRAL + (http://astral.berkeley.edu). + +Files: debian/* +Copyright: © 2007-2008, Morten Kjeldgaard +License: GPL-2+ --- theseus-1.4.3.orig/debian/getexamples +++ theseus-1.4.3/debian/getexamples @@ -0,0 +1,50 @@ +#!/bin/sh +# Get example input files for theseus +# Copyright (C) 2007 Morten Kjeldgaard +# +# This script 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 2.1 of the License, or (at your option) any later +# version. +# +# This script 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 script; if not, write to the Free +# Software Foundation, Inc., 51 Franklin Street, Fifth Floor, +# Boston, MA 02110-1301 USA +set -e + +pdbs="1s40" + +astrals="d1ciha_ d1crja_ d1csua_ d1csxa_ d1kyow_ d1lfma_ d1m60a_ d1u74d_ d1yeba_ d2pcbb_" +#astrals="d1cih__ d1cih__2 d1crj__ d1csu__ d1csx__ d1kyow_ d1lfma_ d1m60a_ d1u74d_ d1yeb__ d2pcbb_" + +# function to fetch entries from the pdb +pdb_fetch () { + for f in $* ; do + wget -q -O $f.pdb.gz ftp://ftp.wwpdb.org:/pub/pdb/data/structures/all/pdb/pdb${f}.ent.gz + gzip -d ${f}.pdb.gz + echo fetched $f.pdb + done +} + +# function to fetch entries from astral +astral_fetch() { + for f in $* ; do + wget -q -O ${f}.pdb http://astral.berkeley.edu/pdbstyle.cgi?id=${f}&output=text + echo fetched $f.pdb + done +} + +savedir=$PWD +cd /tmp +echo Downloading to directory /tmp +pdb_fetch $pdbs +astral_fetch $astrals + +cd $savedir --- theseus-1.4.3.orig/debian/rules +++ theseus-1.4.3/debian/rules @@ -0,0 +1,14 @@ +#!/usr/bin/make -f +# rules file using dh for theseus +# Copyright (C) Andreas Tille +# License: GPL + +%: + dh --with quilt $@ + +override_dh_auto_clean: + dh_quilt_patch + dh_auto_clean + +override_dh_auto_install: + echo "Do not call make install, use dh_install instead" --- theseus-1.4.3.orig/debian/theseus.install +++ theseus-1.4.3/debian/theseus.install @@ -0,0 +1,2 @@ +theseus usr/bin +theseus_align /usr/bin --- theseus-1.4.3.orig/debian/docs +++ theseus-1.4.3/debian/docs @@ -0,0 +1 @@ +debian/citation.bib --- theseus-1.4.3.orig/debian/watch +++ theseus-1.4.3/debian/watch @@ -0,0 +1,3 @@ +version=3 +http://www.theseus3d.org/index.html /src/theseus_(.*).tar.gz + --- theseus-1.4.3.orig/debian/examples +++ theseus-1.4.3/debian/examples @@ -0,0 +1,2 @@ +examples/* +debian/getexamples --- theseus-1.4.3.orig/debian/theseus_align.1 +++ theseus-1.4.3/debian/theseus_align.1 @@ -0,0 +1,71 @@ +.\" Hey, EMACS: -*- nroff -*- +.\" First parameter, NAME, should be all caps +.\" Second parameter, SECTION, should be 1-8, maybe w/ subsection +.\" other parameters are allowed: see man(7), man(1) +.TH THESEUS_ALIGN 1 "November, 2008" +.\" 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 insert n+1 empty lines +.\" for manpage-specific macros, see man(7) +.SH NAME +theseus_align \- quick-and-dirty way to superimpose proteins +.SH SYNOPSIS +.B theseus_align +.RI [ "theseus options" ] +\-f \fIpdbfile1.pdb\fR \fIpdbfile2.pdb\fR ... +.SH OPTIONS +The options given to the script will be passed on to \fBtheseus\fR. For a +complete description, see the man page for \fBtheseus\fR (1). +.SH DESCRIPTION +This manual page briefly documents briefly the script \fBtheseus_align\fR, +designed 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 \fIdoes not\fR perform a structure-based +alignment. +.P +First, the script uses \fBtheseus\fR to create FASTA formatted sequence +files corresponding to the exact protein sequences found in the pdb files +that you supply. +.P +Second, these sequences are aligned using the multiple sequence alignment +program of your choice. The script is 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/ +.P +Third, \fBtheseus\fR performs a superposition of the structures using the +sequence alignment as a guide. +.P +The installed version of \fBtheseus_align\fR uses \fBmuscle\fR (1) for +doing the multiple sequence alignment. If you wish to use one of the other +programs mentioned above, you'll have to copy the script to your own +directory and edit it. +.SH SEE ALSO +\fBtheseus\fR (1), +\fBmuscle\fR (1), +\fBclustalw\fR (1), +\fBt_coffee\fR (1), +\fBkalign\fR (1), +\fBdialign2\fR (1), +\fBmafft\fR (1). +All of these programs can be installed on Debian or Ubuntu systems using +\fBapt-get\fR (8). + +.SH AUTHOR +\fBtheseus_align\fR was written by Douglas L. Theobald, Department of +Biochemistry, Brandeis University. +.\"----- + --- theseus-1.4.3.orig/debian/manpages +++ theseus-1.4.3/debian/manpages @@ -0,0 +1,2 @@ +theseus.1 +debian/theseus_align.1 --- theseus-1.4.3.orig/debian/README.Debian +++ theseus-1.4.3/debian/README.Debian @@ -0,0 +1,16 @@ +Theseus for Debian +================== + + +The getexamples script +---------------------- + +The getexamples script, found in /usr/share/doc/theseus/examples/, +illustrates how data can be retrieved from PDB and Astral services, +for subsequent analysis with theseus. + +Note that some of the data files found in examples/, have a different +SCOP-sid in the most recent release of the Astral database. + + + -- Morten Kjeldgaard , Tue, 18 Nov 2008 23:14:32 +0100 --- theseus-1.4.3.orig/debian/README.source +++ theseus-1.4.3/debian/README.source @@ -0,0 +1,4 @@ +This packages uses the quilt patch system. Please read +/usr/share/doc/quilt/README.source for more information. + + -- Andreas Tille Mon, 31 Aug 2009 14:50:19 +0200 --- theseus-1.4.3.orig/debian/patches/00-makefile.patch +++ theseus-1.4.3/debian/patches/00-makefile.patch @@ -0,0 +1,15 @@ +Fix clean target of original Makefile +Author: Morten Kjeldgaard +Switched to quilt: Andreas Tille + +--- 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 + --- theseus-1.4.3.orig/debian/patches/10_kbsd.patch +++ theseus-1.4.3/debian/patches/10_kbsd.patch @@ -0,0 +1,35 @@ +Purpose: Enable Building on kbsd architecture +Author: Cyril Brulebois , Andreas Tille +Fixes: #542879 + +--- theseus.orig/distfit.h ++++ theseus/distfit.h +@@ -713,7 +713,7 @@ + #ifndef LOGNORMAL_SEEN + #define LOGNORMAL_SEEN + +-#ifdef __linux__ ++#if defined(__linux__) || defined(__GLIBC__) + extern double erf(double x); + #endif + +@@ -1446,7 +1446,7 @@ + #ifndef VONMISES_DIST_SEEN + #define VONMISES_DIST_SEEN + +-#ifdef __linux__ ++#if defined(__linux__) || defined(__GLIBC__) + extern double jn(int n, double x); + #endif + +--- theseus.orig/theseus.h ++++ theseus/theseus.h +@@ -51,7 +51,7 @@ + #include + #include + #include +-#ifdef __linux__ ++#if defined(__linux__) || defined(__GLIBC__) + #include + #endif + #include --- theseus-1.4.3.orig/debian/patches/200-make.inc.patch +++ theseus-1.4.3/debian/patches/200-make.inc.patch @@ -0,0 +1,50 @@ +1. Use ar instead of libtool because of "libtool: unrecognized option `-o'" error + when using libtool (Andreas Tille) +2. Remove -arch options which let gcc fail (Andreas Tille) +3. Add Ubuntu specific build options which work for Debian as well (Morten Kjeldgaard) +Author: Morten Kjeldgaard +Switched to quilt: Andreas Tille + +--- theseus.orig/make.inc ++++ theseus/make.inc +@@ -2,10 +2,10 @@ + # The archiver and the flag(s) to use when building archive (library) + # If you system has no ranlib, set RANLIB = echo. + # +-#ARCH = ar +-ARCH = libtool +-ARCHFLAGS = -o +-#ARCHFLAGS= -rvs ++ARCH = ar ++#ARCH = libtool ++#ARCHFLAGS = -o ++ARCHFLAGS= -rvs + RANLIB = ranlib + + #MACOSX_DEPLOYMENT_TARGET=10.4 +@@ -21,7 +21,7 @@ + INSTALLDIR = /usr/local/bin + OPT = -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer + WARN = -Wall -Werror -pedantic -std=c99 -Wstrict-aliasing=2 +-CFLAGS = $(WARN) -force_cpusubtype_ALL -mmacosx-version-min=10.4 -arch ppc -arch i386 -DNDEBUG ++CFLAGS = $(WARN) -DNDEBUG + CC = /usr/bin/gcc + + +@@ -241,3 +241,16 @@ + # 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 += $(WARN) ++CC = gcc --- theseus-1.4.3.orig/debian/patches/99-theseus_align.sh.patch +++ theseus-1.4.3/debian/patches/99-theseus_align.sh.patch @@ -0,0 +1,47 @@ +Fix path names in shell script to adapt to Debian locations of files +ANTENTION: This patch is currently not used +Authors: Morten Kjeldgaard , Andreas Tille + +--- theseus.orig/theseus_align ++++ theseus/theseus_align +@@ -41,33 +41,33 @@ + # The following six constant strings should be modified to whatever is + # convenient and applicable. + +-theseus="/usr/local/bin/theseus"; # where to find the THESEUS binary executable ++theseus="/usr/bin/theseus"; # where to find the THESEUS binary executable + fastafile="theseus.fasta"; + filemapfile="theseus.filemap"; + alignmentfile="theseus.aln"; + + # for MUSCLE -- http://www.drive5.com/muscle/ +-alignprog="/usr/local/bin/muscle"; ++alignprog="/usr/bin/muscle"; + align_cmd="${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/'"; + + --- theseus-1.4.3.orig/debian/patches/series +++ theseus-1.4.3/debian/patches/series @@ -0,0 +1,4 @@ +00-makefile.patch +200-make.inc.patch +99-theseus_align.sh.patch +10_kbsd.patch