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From: <boc...@su...> - 2006-02-17 00:09:15
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Update of /cvsroot/dev-boconnor/project_logic_analysis/conf In directory sumo.genetics.ucla.edu:/tmp/cvs-serv31072/conf Modified Files: make_profiles_and_run_la_include.xml Log Message: Changes to conf files Index: make_profiles_and_run_la_include.xml =================================================================== RCS file: /cvsroot/dev-boconnor/project_logic_analysis/conf/make_profiles_and_run_la_include.xml,v retrieving revision 1.4 retrieving revision 1.5 diff -C2 -d -r1.4 -r1.5 *** make_profiles_and_run_la_include.xml 16 Feb 2006 08:19:58 -0000 1.4 --- make_profiles_and_run_la_include.xml 17 Feb 2006 00:09:07 -0000 1.5 *************** *** 2,6 **** [% index = index + 1 %] <!-- parses the SIF file to generate a hash of file names and their HC --> ! <step id="[% index %]" active="1" type="module" processor="Nelson::Pipe::Container::Job::SifFileParser"> <input> <item id="sif_file" value="[% sif_file %]"/> --- 2,6 ---- [% index = index + 1 %] <!-- parses the SIF file to generate a hash of file names and their HC --> ! <step id="[% index %]" active="0" type="module" processor="Nelson::Pipe::Container::Job::SifFileParser"> <input> <item id="sif_file" value="[% sif_file %]"/> *************** *** 19,23 **** <!-- reads the hash created by the SIF parser and randomly selects files for 10-90% of the samples --> <!-- FIXME: this creates rounding errors in which the number of files selected is less than it should be! --> ! <step id="[% index %]" active="1" type="module" processor="Nelson::Pipe::Container::Job::RandomlySelectFiles"> <input> <item id="sif_file_hash" value="sif_file_hash"/> --- 19,23 ---- <!-- reads the hash created by the SIF parser and randomly selects files for 10-90% of the samples --> <!-- FIXME: this creates rounding errors in which the number of files selected is less than it should be! --> ! <step id="[% index %]" active="0" type="module" processor="Nelson::Pipe::Container::Job::RandomlySelectFiles"> <input> <item id="sif_file_hash" value="sif_file_hash"/> *************** *** 39,44 **** [% WHILE j < total_number_profiles %] [% FOREACH dir = dirs %] ! <step id="[% index %]" active="1" type="module" processor="Nelson::Pipe::Container::Job::CreateProfiles"> ! <!-- step id="[% index %]" active="1" type="module" processor="Nelson::Pipe::Container::Job::CreateProfiles" execution_type="cluster" --> <input> <item id="file_list_dir" value="data/[% datadir %]/rand_file_lists"/> --- 39,44 ---- [% WHILE j < total_number_profiles %] [% FOREACH dir = dirs %] ! <step id="[% index %]" active="0" type="module" processor="Nelson::Pipe::Container::Job::CreateProfiles"> ! <!-- step id="[% index %]" active="0" type="module" processor="Nelson::Pipe::Container::Job::CreateProfiles" execution_type="cluster" --> <input> <item id="file_list_dir" value="data/[% datadir %]/rand_file_lists"/> *************** *** 62,68 **** [% END %] [% index = index + 1 %] <!-- the next two steps just read all the profiles --> ! <step id="[% index %]" active="1" type="module" processor="Nelson::Pipe::Container::Job::RandomlySelectFiles"> <input> <item id="sif_file_hash" value="sif_file_hash"/> --- 62,69 ---- [% END %] + <!-- large datasets will take a long time to run and need to use the special version of PPLA --> [% index = index + 1 %] <!-- the next two steps just read all the profiles --> ! <step id="[% index %]" active="0" type="module" processor="Nelson::Pipe::Container::Job::RandomlySelectFiles"> <input> <item id="sif_file_hash" value="sif_file_hash"/> *************** *** 76,80 **** </step> [% index = index + 1 %] ! <step id="[% index %]" active="1" type="module" processor="Nelson::Pipe::Container::Job::CreateProfiles"> <input> <item id="file_list_dir" value="data/[% datadir %]/complete_file_list"/> --- 77,81 ---- </step> [% index = index + 1 %] ! <step id="[% index %]" active="0" type="module" processor="Nelson::Pipe::Container::Job::CreateProfiles"> <input> <item id="file_list_dir" value="data/[% datadir %]/complete_file_list"/> *************** *** 83,87 **** <item id="sif_file_hash" value="sif_file_hash"/> <item id="sif_file_hash_storable" value="data/[% datadir %]/sif_hash.storable"/> ! <item id="parse_old_mas5" value="1"/> <item id="start" value="0"/> <item id="end" value="1"/> --- 84,88 ---- <item id="sif_file_hash" value="sif_file_hash"/> <item id="sif_file_hash_storable" value="data/[% datadir %]/sif_hash.storable"/> ! <item id="parse_old_mas5" value="[% parse_old_mas5 %]"/> <item id="start" value="0"/> <item id="end" value="1"/> *************** *** 101,105 **** [% WHILE j < total_number_profiles %] <!-- execution_type="cluster" --> ! <step id="[% index %].[% j %]" active="0" type="module" processor="Nelson::Pipe::Container::Job::PPLARunner" execution_type="cluster"> <input> <item id="entropy_filter" value="3"/> --- 102,106 ---- [% WHILE j < total_number_profiles %] <!-- execution_type="cluster" --> ! <step id="[% index %].[% j %]" active="1" type="module" processor="Nelson::Pipe::Container::Job::PPLARunner" execution_type="cluster"> <input> <item id="entropy_filter" value="3"/> |