[Nelsonlab-cmts] dev-boconnor/project_logic_analysis/conf make_profiles_and_run_la_include.xml,1.4,1.5

[<boc...@su...>]

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"/>