Can I actually just skip executing the migration script, and just install
BWA from the tool shed like I did for other shed tools?? Should be fine I
guess?

Derrick

On Tue, Oct 9, 2012 at 11:49 AM, Derrick Lin <klin...@gmail.com> wrote:

> Hi Greg,
>
> I did another test on a fresh installed galaxy Oct 5 release, I simply
> cloned from the galaxy-dist, start the server once so everything's
> populated, then here was how I ran the migration script and output:
>
> pwbcad@gamma00:galaxy-dist$ sh ./scripts/migrate_tools/0005_tools.sh
> No handlers could be found for logger "galaxy.tools.data"
> /home/pwbcad/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
>   from csamtools import *
> Repositories will be installed into configured tool_path location
>  ../shed_tools
> Adding new row (or updating an existing row) for repository 'bwa_wrappers'
> in the tool_shed_repository table.
>
> The installation process is finished.  You should now remove entries for
> the installed tools from your file named
> ./tool_conf.xml and start your Galaxy server.
>
> I then  checked the migrated_tools_conf.xml but no entries for BWA still.
> Note that I haven't run the previous migration scripts because I don't need
> those tools. Will that be the issue?
>
> Cheers,
> D
>
> On Tue, Oct 9, 2012 at 2:17 AM, Greg Von Kuster <g...@bx.psu.edu> wrote:
>
>> 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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>
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