Dave,

Thanks for that, will pull the latest version and give it a go..

Is there any documentation on these tags and flags??? (tool dependencies
installation)

Cheers,

Franco




On 12/12/12 10:27 PM, "Dave Bouvier" <d...@bx.psu.edu> wrote:

> Franco,
> 
> I see the issue, the target_file flag was introduced in
> 8268:87828175dfe7. If you update to the latest Galaxy dist release, that
> tool dependency xml should work just fine.
> 
>   --Dave B.
> 
> On 2012-12-12 01:53, Franco Caramia wrote:
>> Dave,
>> 
>> It's :
>> 
>> hg log | head
>> changeset:   8153:5dcbbdfe1087
>> tag:         tip
>> user:        Daniel Blankenberg <d...@bx.psu.edu>
>> date:        Tue Nov 06 12:57:23 2012 -0500
>> summary:     Allow rerun to access hidden datasets.
>> 
>> Thanks,
>> 
>> Franco
>> 
>> 
>> On 12/12/12 3:13 PM, "Dave Bouvier" <d...@bx.psu.edu> wrote:
>> 
>>> Franco,
>>> 
>>> You're right, I see a both clean and all rules in the makefile. It looks
>>> almost like it's not finding the expected makefile, I'll have to look
>>> into that in the morning. As for the download_by_url action, it
>>> downloads and extracts the specified file, then changes to the extracted
>>> directory.
>>> 
>>> Could you remind me which changeset revision you're trying to install
>>> this repository in?
>>> 
>>>    --Dave B.
>>> 
>>> On 2012-12-11 23:10, Franco Caramia wrote:
>>>> Hi Dave,
>>>> 
>>>> It does not require it, but it should not fail either as the clean rule is
>>>> in the makefile..
>>>> By removing it I get:
>>>> make: *** No rule to make target `all'. Stop.
>>>> 
>>>> Same problem as before but this time with the 'all' rule...
>>>> I'm not sure what the <action type="download_by_url" tag does..
>>>> Do I need to 'cd' into the unzipped directory?
>>>> 
>>>> Thanks,
>>>> 
>>>> Franco
>>>> 
>>>> 
>>>> On 12/12/12 1:03 PM, "Dave Bouvier" <d...@bx.psu.edu> wrote:
>>>> 
>>>>> Franco,
>>>>> 
>>>>> BEDTools, unlike some other packages, does not require the 'make clean'
>>>>> shell command to compile. If you remove that line, the dependency should
>>>>> install without problems.
>>>>> 
>>>>>     --Dave B.
>>>>> 
>>>>> On 2012-12-11 21:16, Franco Caramia wrote:
>>>>>> Hi list,
>>>>>> 
>>>>>> I got the following tool_dependencies.xml file failing:
>>>>>> 
>>>>>> <?xml version="1.0"?>
>>>>>> <tool_dependency>
>>>>>>       <package name="bedtools" version="2.17.0">
>>>>>>           <install version="1.0">
>>>>>>               <actions>
>>>>>>            <action type="download_by_url"
>>>>>> target_filename="bedtools-2.17.0.tar.gz"
>>>>>>> http://bedtools.googlecode.com/files/BEDTools.v2.17.0.tar.gz</action>
>>>>>>            <action type="shell_command">make clean</action>
>>>>>>            <action type="shell_command">make all</action>
>>>>>>            <action type="move_directory_files">
>>>>>>                <source_directory>bin</source_directory>
>>>>>> 
>>>>>> <destination_directory>$INSTALL_DIR/bin</destination_directory>
>>>>>>            </action>
>>>>>>            <action type="set_environment">
>>>>>>               <environment_variable name="PATH"
>>>>>> action="prepend_to">$INSTALL_DIR/bin</environment_variable>
>>>>>>            </action>
>>>>>>               </actions>
>>>>>>           </install>
>>>>>>           <readme>
>>>>>> GCC version 4.1 or greater is recommended. 3.x versions will typically
>>>>>> not
>>>>>> compile BEDTools
>>>>>>           </readme>
>>>>>>       </package>
>>>>>> </tool_dependency>
>>>>>> 
>>>>>> The error given is:
>>>>>> 
>>>>>> #############################################
>>>>>> make clean
>>>>>> STDOUT
>>>>>> 
>>>>>> #############################################
>>>>>> 
>>>>>> #############################################
>>>>>> make clean
>>>>>> STDERR
>>>>>> make: *** No rule to make target clean'.  Stop.
>>>>>> #############################################
>>>>>> 
>>>>>> I basically just copied the example code from the Galaxy wiki for R:
>>>>>> 
>>>>>> <?xml version="1.0"?>
>>>>>> <tool_dependency>
>>>>>>        <set_environment version="1.0">
>>>>>>            <environment_variable name="R_SCRIPT_PATH"
>>>>>> action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
>>>>>>        </set_environment>
>>>>>>        <package name="R" version="2.15.1">
>>>>>>            <install version="1.0">
>>>>>>                <actions>
>>>>>>                    <action
>>>>>> type="download_by_url">http://CRAN.R-project.org/src/base/R-2/R-2.15.1.ta
>>>>>> r.
>>>>>> gz
>>>>>> </action>
>>>>>>                    <action type="shell_command">./configure
>>>>>> --prefix=$INSTALL_DIR</action>
>>>>>>                    <action type="shell_command">make</action>
>>>>>>                    <action type="set_environment">
>>>>>>                        <environment_variable name="PATH"
>>>>>> action="prepend_to">$INSTALL_DIR/bin</environment_variable>
>>>>>>                    </action>
>>>>>>                </actions>
>>>>>>            </install>
>>>>>>            <readme>
>>>>>> You need a FORTRAN compiler or perhaps f2c in addition to a C compiler
>>>>>> to build R.
>>>>>>            </readme>
>>>>>>        </package>
>>>>>> </tool_dependency>
>>>>>> 
>>>>>> I have found no documentation to what the tag <action
>>>>>> type="download_by_url"> does...
>>>>>> I have asumed it downloads, unzips and moves into the unzipped
>>>>>> directory.. But apparently it doesn┬╣t..
>>>>>> 
>>>>>> Any advice on this or at least a link to the pertinent documentation??
>>>>>> 
>>>>>> Thanks a lot in advance...
>>>>>> 
>>>>>> Franco
>>>>>> 
>>>>>> 
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