Glad to help. The only further thing I'd say is do a lot testing. Galaxy is a large,
complex piece of software with some bits hard coded, some bits configurable, and there are
decentralized policies or behaviors. So just be sure making a change in one place, like
commenting out that section, doesn't negatively impact some other functionality you or
your users may want.
Best of luck,
From: Brent Pedersen [bpederse(a)gmail.com]
Sent: Friday, September 30, 2011 1:15 PM
To: Paniagua, Eric
Subject: Re: [galaxy-user] upload zip file to custom tool
On Fri, Sep 30, 2011 at 10:41 AM, Paniagua, Eric <epaniagu(a)cshl.edu> wrote:
I've encountered this behavior too. I don't know the ultimate reason or purpose,
but compressed files (especially zip) are handled in very specific, restricted ways by the
upload framework. The behavior you describe is hard coded into the upload tool.
For example, check out the use of the 'zipfile' module in
tools/data_source/upload.py. That file (tool) will actually try to sniff your file even
if you've set the file type in upload. See the data flow (or data non-flow) through
local variable 'ext' in tools/data_source/upload.py:add_file(). Odd and
restrictive policy for treatment of compressed files can be seen elsewhere in the codebase
too, including test/base/twilltestcase.py:TwillTestCase.verify_dataset_correctness().
My advice (and this is also basically the advice Nate gave me) is to fork your own copy
of the upload tool to make a version that works for your files.
Nate may have more to say on the matter.
Eric, thanks for pointing me to that file. I just commented out the
unzip section for now and
also changed one section that was causing it to show "...inappropriate
content" and it seems to
be working now.
From: galaxy-user-bounces(a)lists.bx.psu.edu [galaxy-user-bounces(a)lists.bx.psu.edu] on
behalf of Brent Pedersen [bpederse(a)gmail.com]
Sent: Friday, September 30, 2011 11:59 AM
Subject: [galaxy-user] upload zip file to custom tool
I have followed the wiki and built a custom tool on a local galaxy installation.
One of the inputs is a zip file. It seems galaxy automatically unpacks
it and keeps only
the first file. Is there any way I can tell galaxy not to unzip the file?
I tried to register .zip as a datatype, but that didn't seem to change
thanks for any help.
$tool.xml is below in case it helps.
<command interpreter="python">charmqc.py $xyszip $output
<param format="xys.zip" name="xyszip" type="data"
<param type="select" name="organism"
<option value="Human">Human (hg18)</option>
<option value="Mouse">Mouse (mm8)</option>
<data format="data" name="output" />
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