Hi David,
With the exception of requiring versions strings in <requirement> tags in the
tool config in order to enable versioned tool dependency installation (which is
documented in the tool shed wiki at
http://wiki.g2.bx.psu.edu/Tool%20Shed#Automatic_third-party_tool_dependency_installation_and_compilation_with_installed_repositories),
this is the first change to the way Galaxy tool configs should be written.
I'll get a wiki put together for this new enhancement as soon as possible. I'm
hoping to have it as part of the next Galaxy dist release when the feature is
released.
Greg Von Kuster
On Sep 12, 2012, at 1:47 PM, David Hoover wrote:
> On the topic of toolshed tools, is there any documented guidance about how to
> create a tool for the toolshed? There is some syntactical help on the wiki,
> but no comprehensive guide.
>
> On Sep 12, 2012, at 1:41 PM, Greg Von Kuster wrote:
>
>> It'll be available in Galaxy central sooner than Galaxy dist. I'll send you
>> an email when I commit it.
>>
>> On Sep 12, 2012, at 1:31 PM, David Hoover wrote:
>>
>>> Will it be available through galaxy-dist or galaxy-central? I have started
>>> using the galaxy-central repository just to be on the bleeding edge.
>>>
>>> On Sep 12, 2012, at 1:15 PM, Greg Von Kuster wrote:
>>>
>>>> Hello David,
>>>>
>>>> This is not currently possible, but will be available in the next Galaxy
>>>> distribution release, currently scheduled for about 10 days from now. You
>>>> will include a tool_dependencies.xml file in your tool shed repository
>>>> that looks something like the following.
>>>>
>>>> <?xml version="1.0"?>
>>>> <tool_dependency>
>>>> <set_environment version="1.0">
>>>> <environment_variable name="JAVA_JAR_PATH"
>>>> action="set_to">$INSTALL_DIR</environment_variable>
>>>> </set_environment>
>>>> </tool_dependency>
>>>>
>>>> Your tool will find the required files via the defined JAVA_JAR_PATH by
>>>> using a <requirements> tag set in the tool config, something like this:
>>>>
>>>> <requirements>
>>>> <requirement type="set_environment">JAVA_JAR_PATH </requirement>
>>>> </requirements>
>>>>
>>>> The <command> tag in the tool config would be something like this:
>>>>
>>>> <command interpreter="python">
>>>> python_wrapper.py $JAVA_JAR_PATH/some_file.jar $param1 $param2...
>>>> </command>
>>>>
>>>> I'm close to having this working, so if you are interested in testing
>>>> before the next Galaxy dist release, let me know and I'll tell you when
>>>> the Galaxy central repository has the new feature.
>>>>
>>>> Thanks!
>>>>
>>>> Greg Von Kuster
>>>>
>>>>
>>>> On Sep 12, 2012, at 1:00 PM, David Hoover wrote:
>>>>
>>>>> Are there any environment variables that are honored by toolshed
>>>>> installed tools? I tried creating a tool that uses
>>>>> ${GALAXY_DATA_INDEX_DIR} or $GALAXY_HOME, then uploaded it the test
>>>>> toolshed, then installed it automatically. Neither of these resolved to
>>>>> what I expected. I don't want to hard-code the path in the xml tool
>>>>> file, but rather have a default location for other executables and jar
>>>>> files. How should this best be done?
>>>>>
>>>>> David Hoover
>>>>> Helix Systems Staff
>>>>> ___________________________________________________________
>>>>> Please keep all replies on the list by using "reply all"
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>>>>> http://lists.bx.psu.edu/
>>>>
>>>
>>>
>
>
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