Hi Derrick,

The wiki page to which you refer describes the manual way that the Galaxy admin 
can install tool dependencies (using a manual process).  The tool shed 
automatically does everything to install repositories, tools, tool 
dependencies, datatypes, and other repository contents.  If you have not yet 
read the tool shed wiki, you should become familiar with all of the features it 
provides if you plan to continue using it.  

The link to the entire tool shed wiki is:

http://wiki.g2.bx.psu.edu/Tool%20Shed

For automatic installation of tool dependencies, see this specific section of 
the tool shed wiki:

http://wiki.g2.bx.psu.edu/ToolShedToolFeatures#Automatic_third-party_tool_dependency_installation_and_compilation_with_installed_repositories

Sorry for the confusion the Admin wiki you were using caused.

Greg Von Kuster


On Oct 10, 2012, at 12:07 AM, Derrick Lin wrote:

> Okay,
> 
> I found the button for installing the dependencies. The files are installed:
> 
> galaxy-dist/tool_dependency_dir/bwa/0.5.9/devteam/bwa_wrappers/ffa8aaa14f7c
> 
> Quite different from what the wiki states..
> 
> http://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies
> 
> Derrick
> 
> On Wed, Oct 10, 2012 at 2:43 PM, Derrick Lin <klin...@gmail.com> wrote:
> Thanks Greg,
> 
> Indeed, I tried to be smart and removed the entries from tool conf xml before 
> running the script. :)
> 
> About the missing dependencies, I still couldn't make it happy. I have added:
> 
> $GALAXY_ROOT/tool_dependency_dir/bwa/0.5.9/env.sh
> 
> and add appropriate export PATH inside the env.sh, restart the galaxy but it 
> still complains about the missing dependencies.
> 
> Is there an official way to  setup the files to meet the dependencies 
> requirement defined in shed tool's xml?
> 
> Cheers,
> Derrick
> 
> On Tue, Oct 9, 2012 at 9:26 PM, Greg Von Kuster <g...@bx.psu.edu> wrote:
> Hi Derrick,
> 
> Yes, this approach will work fine.
> 
> Greg Von Kuster
> 
> On Oct 8, 2012, at 11:44 PM, Derrick Lin wrote:
> 
>> Can I actually just skip executing the migration script, and just install 
>> BWA from the tool shed like I did for other shed tools?? Should be fine I 
>> guess?
>> 
>> Derrick
>> 
>> On Tue, Oct 9, 2012 at 11:49 AM, Derrick Lin <klin...@gmail.com> wrote:
>> Hi Greg,
>> 
>> I did another test on a fresh installed galaxy Oct 5 release, I simply 
>> cloned from the galaxy-dist, start the server once so everything's 
>> populated, then here was how I ran the migration script and output:
>> 
>> pwbcad@gamma00:galaxy-dist$ 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
>>> ___________________________________________________________
>>> Please keep all replies on the list by using "reply all"
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>>> 
>>>  http://lists.bx.psu.edu/
>> 
>> 
>> 
> 
> 
> 

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