Hmm, this is a tricky case. I can think of three possible solutions. A "don't unzip" checkbox on the upload form (but this may be confusing to people who aren't aware that only a few specialized tools would be able to deal with the zipped files). Let Galaxy auto-detect the file type based on extension, if it's actually a zip file. Like Python eggs and self-extracting exes, it could be a zip file which has been renamed to some new extension. Force users to select the correct file type from the drop-down, or else if it's detected as a zip it's always unpacked. This is the way we did it for a few older tools. --nate Erick Antezana wrote:
Hi Nate,
actually, I wanted to develop a couple of tools (to be further used from within a workflow) that could take as input a ZIP-formatted file and then process it with other tools. The motivation was due to two data providers that sent out data in ZIP :-( and not GZ... So we couldn't ask our users to UNZIP them (lots of files) and afterwards to GZIP them... Anyway, I manage to get a *compromise* with our Galaxy users and we will use GZ-formatted files (thus the ZIP ones will become GZ...).
thanks, Erick
On 31 March 2010 18:32, Nate Coraor <nate@bx.psu.edu> wrote:
Erick Antezana wrote:
Hi Nate,
I am afraid there is still an issue while trying to upload a directory of files (containing ZIP files). My ZIP files are not erased anymore from my "user_library_import_dir". But I still get the message:
"Job error (click name for more info)" Hi Erick,
Do you have tools that work directly with unmodified ZIP files? We don't have support for unpacking ZIP files during upload yet (this is the cause of the "inappropriate content" message), although work on this is in progress.
Thanks, --nate
and after clicking on any of those files, I get:
Message:
Uploaded by: erick@mydomain.com
Date uploaded: 2010-03-31
Build: ?
Miscellaneous information: The uploaded file contains inappropriate content
error
Any suggestions?
thanks in advance, Erick p.s. my changeset: 3560:4c95f1a101f1
On 23 March 2010 17:45, Nate Coraor <nate@bx.psu.edu> wrote:
Hi Erick,
Thanks for reporting this, the deletion bug has been fixed in changeset 3556:8f6fa47b21c4.
--nate
Erick Antezana wrote:
Hi,
It seems there is a (serious) bug while "Adding datasets" via the "Upload directory of files" (with or without copying the data into Galaxy (3545:2590120aed68), i.e. (un)tick the 'No' box) if the files are in ZIP format. Actually the files get erased from the filesystem.
In the "information" column, I get:
Job error (click name for more info)
Then, after clicking on the file name:
Information about 2010.fastq.zip Message:
Uploaded by: erick@mydomain.com Date uploaded: 2010-03-23 Build: ? Miscellaneous information: The uploaded file contains inappropriate content error
We have no problems with adding unzipped files...
thanks, Erick _______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user