Any ideas anyone?<div><br clear="all">Philip Mabon<br>Senior Bioinformatician<br>National Microbiology Laboratory<br>Public Health Agency of Canada <br>
<br><br><div class="gmail_quote">On Tue, Aug 21, 2012 at 10:34 AM, Philip Mabon <span dir="ltr">&lt;<a href="mailto:philipmabon@gmail.com" target="_blank">philipmabon@gmail.com</a>&gt;</span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="color:rgb(34,34,34);font-size:13px;font-family:arial,sans-serif">I just upgrade our galaxy to the latest release :  7487:be81990d148a and ran the migration tool script for freebayes. </div>
<div style="color:rgb(34,34,34);font-size:13px;font-family:arial,sans-serif"><br></div><div style="color:rgb(34,34,34);font-size:13px;font-family:arial,sans-serif">
I received the following error:</div><div style="color:rgb(34,34,34);font-size:13px;font-family:arial,sans-serif"><br></div><div style="color:rgb(34,34,34);font-size:13px;font-family:arial,sans-serif">
<div>No handlers could be found for logger &quot;galaxy.tools&quot;</div><div>/opt/galaxy/galaxy_dist/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/pysam/__init__.py:1: RuntimeWarning: __builtin__.file size changed, may indicate binary incompatibility</div>

<div>  from csamtools import *</div><div>Repositories will be installed into configured tool_path location  ../shed_tools</div><div>Adding new row (or updating an existing row) for repository &#39;freebayes&#39; in the tool_shed_repository table.</div>

<div>Traceback (most recent call last):</div><div>  File &quot;./scripts/migrate_tools/migrate_tools.py&quot;, line 21, in &lt;module&gt;</div><div>    app = MigrateToolsApplication( sys.argv[ 1 ] )</div><div>  File &quot;/opt/galaxy/galaxy_dist/lib/galaxy/tool_shed/migrate/common.py&quot;, line 150, in __init__</div>

<div>    install_dependencies=install_dependencies )</div><div>  File &quot;/opt/galaxy/galaxy_dist/lib/galaxy/tool_shed/install_manager.py&quot;, line 37, in __init__</div><div>    self.install_repository( repository_elem, install_dependencies )</div>

<div>  File &quot;/opt/galaxy/galaxy_dist/lib/galaxy/tool_shed/install_manager.py&quot;, line 262, in install_repository</div><div>    install_dependencies=install_dependencies )</div><div>  File &quot;/opt/galaxy/galaxy_dist/lib/galaxy/tool_shed/install_manager.py&quot;, line 150, in handle_repository_contents</div>

<div>    repository_tools_tups = get_repository_tools_tups( self.app, metadata_dict )</div><div>  File &quot;/opt/galaxy/galaxy_dist/lib/galaxy/util/shed_util.py&quot;, line 1077, in get_repository_tools_tups</div><div>    tool = app.toolbox.load_tool( os.path.abspath( relative_path ), guid=guid )</div>

<div>  File &quot;/opt/galaxy/galaxy_dist/lib/galaxy/tools/__init__.py&quot;, line 452, in load_tool</div><div>    return ToolClass( config_file, root, self.app, guid=guid )</div><div>  File &quot;/opt/galaxy/galaxy_dist/lib/galaxy/tools/__init__.py&quot;, line 790, in __init__</div>

<div>    self.parse( root, guid=guid )</div><div>  File &quot;/opt/galaxy/galaxy_dist/lib/galaxy/tools/__init__.py&quot;, line 961, in parse</div><div>    self.parse_inputs( root )</div><div>  File &quot;/opt/galaxy/galaxy_dist/lib/galaxy/tools/__init__.py&quot;, line 1045, in parse_inputs</div>

<div>    display, inputs = self.parse_input_page( page, enctypes )</div><div>  File &quot;/opt/galaxy/galaxy_dist/lib/galaxy/tools/__init__.py&quot;, line 1447, in parse_input_page</div><div>    inputs = self.parse_input_elem( input_elem, enctypes )</div>

<div>  File &quot;/opt/galaxy/galaxy_dist/lib/galaxy/tools/__init__.py&quot;, line 1514, in parse_input_elem</div><div>    case.inputs = self.parse_input_elem( case_elem, enctypes, context )</div><div>  File &quot;/opt/galaxy/galaxy_dist/lib/galaxy/tools/__init__.py&quot;, line 1470, in parse_input_elem</div>

<div>    group.inputs = self.parse_input_elem( elem, enctypes, context )</div><div>  File &quot;/opt/galaxy/galaxy_dist/lib/galaxy/tools/__init__.py&quot;, line 1540, in parse_input_elem</div><div>    param = self.parse_param_elem( elem, enctypes, context )</div>

<div>  File &quot;/opt/galaxy/galaxy_dist/lib/galaxy/tools/__init__.py&quot;, line 1552, in parse_param_elem</div><div>    param = ToolParameter.build( self, input_elem )</div><div>  File &quot;/opt/galaxy/galaxy_dist/lib/galaxy/tools/parameters/basic.py&quot;, line 176, in build</div>

<div>    return parameter_types[param_type]( tool, param )</div><div>  File &quot;/opt/galaxy/galaxy_dist/lib/galaxy/tools/parameters/basic.py&quot;, line 1361, in __init__</div><div>    ToolParameter.__init__( self, tool, elem )</div>

<div>  File &quot;/opt/galaxy/galaxy_dist/lib/galaxy/tools/parameters/basic.py&quot;, line 43, in __init__</div><div>    self.validators.append( validation.Validator.from_element( self, elem ) )</div><div>  File &quot;/opt/galaxy/galaxy_dist/lib/galaxy/tools/parameters/validation.py&quot;, line 23, in from_element</div>

<div>    return validator_types[type].from_element( param, elem )</div><div>  File &quot;/opt/galaxy/galaxy_dist/lib/galaxy/tools/parameters/validation.py&quot;, line 279, in from_element</div><div>    tool_data_table = param.tool.app.tool_data_tables[ table_name ]</div>

<div>  File &quot;/opt/galaxy/galaxy_dist/lib/galaxy/tools/data/__init__.py&quot;, line 25, in __getitem__</div><div>    return self.data_tables.__getitem__( key )</div><div>KeyError: &#39;sam_fa_indexes&#39;</div></div>
<div style="color:rgb(34,34,34);font-size:13px;font-family:arial,sans-serif">
<br></div><div style="color:rgb(34,34,34);font-size:13px;font-family:arial,sans-serif"><br></div><div style="color:rgb(34,34,34);font-size:13px;font-family:arial,sans-serif">
What happen is that the freebayes itself installs correctly into the shed_tools/<a href="http://toolshed.g2.bx.psu.edu/repos/devteam/*" style="color:rgb(17,85,204)" target="_blank">toolshed.g2.bx.psu.edu/repos/devteam/*</a> but the dependency on samtools 1.1.8 fails.</div>

<div style="color:rgb(34,34,34);font-size:13px;font-family:arial,sans-serif"><br></div><div style="color:rgb(34,34,34);font-size:13px;font-family:arial,sans-serif">
The value &#39;sam_fa_indexes&#39; is present in the tool_data_table_conf.xml  and I know it works since all my samtools are functional.</div><div style="color:rgb(34,34,34);font-size:13px;font-family:arial,sans-serif">
<br></div><div style="color:rgb(34,34,34);font-size:13px;font-family:arial,sans-serif">The status column for the freebayes entry in the database is &#39;Cloning&#39;. </div><div style="color:rgb(34,34,34);font-size:13px;font-family:arial,sans-serif">

<br></div><div style="color:rgb(34,34,34);font-size:13px;font-family:arial,sans-serif">I get the same error if I try to install freebayes thru the web front end. ( Had to delete the row in the db and remove the freebayes install directory)</div>

<div style="color:rgb(34,34,34);font-size:13px;font-family:arial,sans-serif"><br></div><div style="color:rgb(34,34,34);font-size:13px;font-family:arial,sans-serif">
Any ideas Greg?</div><div style="color:rgb(34,34,34);font-size:13px;font-family:arial,sans-serif"><br></div><div style="color:rgb(34,34,34);font-size:13px;font-family:arial,sans-serif">
Thanks!</div><br clear="all" style="color:rgb(34,34,34);font-size:13px;font-family:arial,sans-serif"><span style="color:rgb(34,34,34);font-size:13px;font-family:arial,sans-serif">Philip Mabon (Takadonet)</span><br style="color:rgb(34,34,34);font-size:13px;font-family:arial,sans-serif">

<span style="color:rgb(34,34,34);font-size:13px;font-family:arial,sans-serif">Senior Bioinformatician</span><br style="color:rgb(34,34,34);font-size:13px;font-family:arial,sans-serif">
<span style="color:rgb(34,34,34);font-size:13px;font-family:arial,sans-serif">National Microbiology Laboratory</span><br style="color:rgb(34,34,34);font-size:13px;font-family:arial,sans-serif">
<span style="color:rgb(34,34,34);font-size:13px;font-family:arial,sans-serif">Public Health Agency of Canada</span>
</blockquote></div><br></div>