Hi Greg, Jean-Frédéric,

I'm returning to this old thread rather than starting a new one,
since it is nicely aligned with something I wanted to raise.

On Tue, Feb 19, 2013 at 2:23 PM, Greg Von Kuster <g...@bx.psu.edu> wrote:
> Hello Jean-Frédéric,
> Sorry for the delay in this response.  Please see my inline comments.
> On Feb 8, 2013, at 10:33 AM, Jean-Frédéric Berthelot wrote:
>> Hi list,
>> The tool I am currently wrapping has built-in data, which may be used by the
>> tool users (through a relevant <from_data_table> + .LOC file configuration).
>> They are .fasta databases which are rather small and are thus bundled in the
>> tool distribution package.
>> Thanks to the tool_dependencies.xml file, said distribution package is
>> downloaded at install time, code is compiled, and since they are here,
>> the data files are copied to $INSTALL_DIR too, ready to be used.
>> After that, the user still has to edit tool-data/my_fancy_data_files.loc ;
>> but the thing is, during the install I know where these data files are
>> (since I copied those there), so I would like to save the user the trouble
>> and set up this file automagically.
>> I would have two questions:
>> 1/ Is it okay to have tool built-in data files in $INSTALL_DIR, or would
>> it be considered bad practice?
> This is difficult to answer.  Generally, data files should be located in a
> shared location so that other tools can access them as well.  However, there
> are potentially exceptions to this that are acceptable.  The fact that the
> fasta data files are small and you are using a tool_dependencies.xml file to
> define a relationship to them for your tools is a good approach because it
> allows the data files to be used by other tools in separate repositories via
> a complex repository dependency definition in the remote repository.
> If these fasta data files are available for download via a clone or a url,
> then in the near future the new Galaxy Data Manager (which uses a new,
> special category of Galaxy tools which are of type "data_manager") may be
> useful in this scenario.  Data Manager tools can be associated with tools in
> a repository like yours using repository dependency definitions, so they
> will be installed along with the selected repository.  These data manager
> tools allow for specified data to be installed into the Galaxy environment
> for use by tools.  This new component is not yet released, but it is close.
> In the meantime, your approach is the only way to make this work.
> If your files are not downloadable, then we might plan to allow simplified
> bootstrapping of .loc files in the tol-data directory with files included in
> the repository.  This would take some planning, and it's availability would
> not be in the short term

Any news Greg? I see there is an empty page on the wiki here:

And some actual content here:

>> 2/ Is there a way to set up the tool-data/my_fancy_data_files.loc during the
>> install? Here are the options I though of:
>> *shipping a “real” my_fancy_data_files.loc.sample with the good paths
>> already set-up, which is going to be copied as the .loc file (a rather ugly
>> hack)
> Assuming you use a file name that is not already in the Galaxy tool-data
> subdirectory, the above approach is probably the only way you can do this in
> a fully automated right now.  Again, when the new Data Manager is released,
> it will handle this kind of automated configuration.  But in the meantime,
> manual intervention is generally required to add the information to
> appropriate .loc files in the tool-data directory.

Is that still the case today?

>> *using more <action type="shell_command"> during install to create
>> my_fancy_data_files.loc (but deploying this file it is not part of the tool
>> dependency install per se)
> I advise against the above approach.  The "best practice" use of tool
> dependency definitions is to restrict movement of files to location within
> the defined $INSTALL_DIR (the installation directory of the tol dependency
> package) or $REPOSITORY_INSTALL_DIR (the installation directory of the
> repository), which is set at installation time.  Hard-coding file paths in
> <action> tags is fragile, and not recommeded.
>> *variant of the previous : shipping my_fancy_data_files.loc as part of the
>> tool distribution package, and copy it through shell_command (same concern
>> than above).
> The above approach is not recommended either - same issue as above.

I may not be following your recommendation - in a couple of tools
I provide a functional working *.loc.sample file which is installed
as the default *.loc file.

I do this in both the Blast2GO and EffectiveT3 wrappers, but in
both cases I've avoided the need for absolute paths (and the
worry about where to put the files) and used relative paths
(and put the files in $INSTALL_DIR). This works quite well:


However, for something like NCBI BLAST setting up some test
databases via the <action> tags would be a bit more fiddly -
although it could let me increase the tools' test coverage.

As an aside, I've asked before about why the function tests look
at *.loc rather than *.loc.sample and not had a clear answer. As
soon as the local administrator edits the provided default *.loc
files, this could break functional tests using the *.loc.sample
values. The simple fix is for the test framework to preferentially
load the *.loc.sample file if present:




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