Rosetta

Version 9 (Anton Vasetenkov, 13.01.2015 00:28)

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h1. Rosetta-Tips
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{{toc}}
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h3. Installation
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При компиляции в Ubuntu 14.10 c OpenMpi возникает ошибка:
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<pre>
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src/protocols/wum2/EndPoint.cc:21:42: error: a function call cannot appear in a constant-expression
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src/protocols/wum2/EndPoint.cc:21:44: error: template argument 1 is invalid
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</pre>
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Антон Васетенков предлагает:
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<pre><code class="ruby">
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// -*- mode:c++;tab-width:2;indent-tabs-mode:t;show-trailing-whitespace:t;rm-trailing-spaces:t -*-
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// vi: set ts=2 noet:
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//
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// (c) Copyright Rosetta Commons Member Institutions.
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// (c) This file is part of the Rosetta software suite and is made available under license.
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// (c) The Rosetta software is developed by the contributing members of the Rosetta Commons.
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// (c) For more information, see http://www.rosettacommons.org. Questions about this can be
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// (c) addressed to University of Washington UW TechTransfer, email: license@u.washington.edu.
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/// @file    protocols/wum2/EndPoint.cc
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/// @brief   Non MPI version of EndPoint
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/// @details This class is required because SingleNode role needs to use an EndPoint that is not MPI dependent (ie just a wrapper for 2 queues)
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/// @author  Ken Jung
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//anton added this
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#include <boost/cstdint.hpp>
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#include <protocols/wum2/EndPoint.hh>
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#include <protocols/wum2/WorkUnit.hh>
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namespace protocols {
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namespace wum2 {
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//anton commented this
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//EndPoint::EndPoint( boost::function < uint64_t () > role_available_mem  ) : role_available_mem_( role_available_mem) {}
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//anton added this
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EndPoint::EndPoint( boost::function < boost::uint64_t () > role_available_mem ) : role_available_mem_( role_available_mem) {}
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} // wum2
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} // protocols
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</pre>
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h3. Fragments
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Генерация
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<pre>
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/home/domain/anur/progs/rosseta/main/source/bin/fragment_picker.default.linuxgccrelease -in:file:fasta 1.fasta -in:file:vall /home/domain/anur/progs/rosseta/tools/fragment_tools/vall.apr24.2008.extended.gz -out::file::frag_prefix pep-1 -frags::frag_sizes 9 5 3
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</pre>
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Если последовательность вашего белка идёт не первой цепью, то надо сдвинуть остатки в файле фрагментов:
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<pre>
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cp ~/progs/rosseta/demos/protocol_capture/2010/FlexPepDock_AbInitio/scripts/frags/shift.sh .
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./shift.sh  pep-1.200.3mers 276 > pep-1.200.shift.3mers
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</pre>
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h3. Запуск MPI версии на Lomonosv 
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Тут используется 48 ядер и module openmpi
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<pre>
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sbatch -n 48 -o log.abinitio.n48 -t 3000  ompi /home/users/golovin/progs/rosetta_2013wk40_bundle/main/source/bin/FlexPepDocking.mpi.linuxgccrelease @flags.abinitiore
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</pre>
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h3. Опции запуска
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https://www.rosettacommons.org/docs/latest/full-options-list.html