Hi Derrick,

I am not able to reproduce this behavior, so it's difficult to tell what 
problem may have occurred that resulted in the entries for the bwa tools to not 
be added to you migrated_tools_conf.xml file.  Choosing to install or not 
install tool dependences makes no difference in whether the repository is 
installed and the tools are properly configured in the migrated_tools_conf.xml 
file and subsequently loaded into the Galaxy tool panel.

Can you try manually adding the following sections to your 
migrated_tools_conf.xml file and see if that solves your problem (of course, 
you can change the section id and name attributes if you want or eliminate the 
section altogether).

<section id="solexa_tools" name="NGS: Mapping" version="">
        <tool 
file="../shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/ffa8aaa14f7c/bwa_wrappers/bwa_wrapper.xml"
 guid="toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3">
            <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
            <repository_name>bwa_wrappers</repository_name>
            <repository_owner>devteam</repository_owner>
            
<installed_changeset_revision>ffa8aaa14f7c</installed_changeset_revision>
            
<id>toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3</id>
            <version>1.2.3</version>
            </tool>
    <tool 
file="../shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/ffa8aaa14f7c/bwa_wrappers/bwa_color_wrapper.xml"
 
guid="toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_color_wrapper/1.0.2">
            <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
            <repository_name>bwa_wrappers</repository_name>
            <repository_owner>devteam</repository_owner>
            
<installed_changeset_revision>ffa8aaa14f7c</installed_changeset_revision>
            
<id>toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_color_wrapper/1.0.2</id>
            <version>1.0.2</version>
            </tool>
    </section>

Greg Von Kuster


On Oct 8, 2012, at 1:55 AM, Derrick LIN wrote:

> Hi guys,
> 
> I have updated the galaxy to Oct 5 dist, and BWA has been reinstalled via the 
> migration script. However, I couldn't find any entry has been added in 
> migrated_tools_conf.xml (thus the BWA tools are not display in the tool 
> panel).
> 
> I check in the admin "Installed tool shed repositories" section and BWA repos 
> status is "Installed, missing dependencies", is that why it didn't get added 
> into the migrated_tools_conf.xml?
> 
> I have had BWA 0.5.9-r16 in path, and been used by the old BWA wrapper 
> without an issue before. How can I fix this dependencies issue for a Shed 
> Tool? Should I add something like:
> 
> <tool_dependency_dir>/bowtie/0.12.7/env.sh
> 
> thanks,
> Derrick
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