Thanks very much for your wiki editing contributions - the particular page has been and
continues to be on my list for making enhancements, and I'm currently planning on
making some additions this week.
I apologize for the difference in how the extraction directories are determined for tar
and zip archives. The use of the target_filename attribute for tar archives is a recent
enhancement that was required for migrating the lastz and bowtie tools from the Galaxy
distribution, and I have not yet had a chance to update the wiki page accordingly (I will
attempt to do so this week).
The tool_dependency.xml definitions have evolved enough that they are sufficient for
defining the process for many 3rd party tool dependencies. However, they will continue to
be refined as additional dependencies are discovered that cannot be installed using the
current definitions. I will continue to update the tool shed wiki page as these
definition tag sets evolve.
Thanks very much for your message and your contributions.
Greg Von Kuster
On Jan 30, 2013, at 10:49 AM, Jean-Frédéric Berthelot wrote:
When working to get a tool wrapper Toolshed-ready, I have explored how tool dependencies
installation works, especially the download_by_url feature.
I have summarised my understanding on the Wiki (hope this is clear and accurate):
The difference of behaviour when dealing with a Tar and a Zip file lies in the methods
tar_extraction_directory() and zip_extraction_directory() (in ), which try to locate
the deflated files:
* zip_extraction_directory() counts the number of non- .zip “files” in the current
directory. If more than one, the current path is returned ; if one, this “file” is assumed
to be the deflated directory, and the full path to this directory is returned. The
file_name variable (set to the name of the downloaded file) is not used.
* tar_extraction_directory() which takes the name of the downloaded_file and removes the
extension. If a subdirectory of that name exists, it is returned. Otherwise, if the full
path to the downloaded file exists, the current path is returned. Otherwise, an exception
This difference of behaviour can be very confusing. My wrapper local installations kept
failing because for my tool, the deflated directory name did not match the tar.gz name. I
was confused because I was using the bowtie wrapper  as an example, where it is not an
The obvious workaround is to use the target_filename attribute to have the downloaded
archive name match the subdirectory name (which I have done, and it works perfectly now).
But I was wondering if it would be a good idea to harmonize both methods behaviour?
(P.S. As I am not very familiar yet with the Galaxy development process, I believe
posting here is appropriate ; but I’d be happy to open an issue − on the Trello if I am
not mistaken? − if needed.)
Bonsai Bioinformatics group
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