Re: [galaxy-dev] [galaxy-user] Tool without input parameters
Or just add a dummy input parameter, like so: ========= <inputs> <param name="dummy" type="text" label="Don't touch me" /> </inputs> <outputs> <data format="html" name="output" /> </outputs> ========= It looks silly, but it works just fine (we have couple of tools like that ;) ). -gordon Gunnar Raetsch wrote, On 01/15/2010 07:49 AM:
Hi,
that would be indeed a useful feature...
What I did some time ago is to let the user choose some example data (e.g. for different organisms), that will be generated into the history.
Then you have some input, outputs and can write the overview in the tool description.
Cheers, Gunnar
On 15.01.2010, at 13:06, Jelle Scholtalbers wrote:
Hi,
Is there a way to provide a tool through galaxy that doesn't need any input parameters? If I just don't specify a parameter I get an error: "AttributeError: Tool instance has no attribute 'inputs'" Specifying a hidden input parameter will load the xml, but in galaxy it won't show a tool overview or execute the tool for you when you click on its name.
Cheers, Jelle
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The fact that a tool with no inputs causes an error is definitely a bug and should be fixed. (Also surprising since we have tools in Galaxy already that have no inputs, e.g. the "Get Microbial Data" tool). On Jan 15, 2010, at 10:17 AM, Assaf Gordon wrote:
Or just add a dummy input parameter, like so:
========= <inputs> <param name="dummy" type="text" label="Don't touch me" /> </inputs> <outputs> <data format="html" name="output" /> </outputs> =========
It looks silly, but it works just fine (we have couple of tools like that ;) ).
-gordon
Gunnar Raetsch wrote, On 01/15/2010 07:49 AM:
Hi,
that would be indeed a useful feature...
What I did some time ago is to let the user choose some example data (e.g. for different organisms), that will be generated into the history.
Then you have some input, outputs and can write the overview in the tool description.
Cheers, Gunnar
On 15.01.2010, at 13:06, Jelle Scholtalbers wrote:
Hi,
Is there a way to provide a tool through galaxy that doesn't need any input parameters? If I just don't specify a parameter I get an error: "AttributeError: Tool instance has no attribute 'inputs'" Specifying a hidden input parameter will load the xml, but in galaxy it won't show a tool overview or execute the tool for you when you click on its name.
Cheers, Jelle
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Hi, I have recently updated our galaxy install running on a cluster with the latest changesets. A new python egg was added: pysam-0.1.1-py2.4-linux-x86_64.egg. This egg requires glib to be upgraded to GLIBC_2.7, and galaxy will not start without it. Due to constraints on our cluster we are not allowed to update glib above version 2.5. I have rolled back the update to try to get Galaxy running but now I need to remove this python egg. Simply deleting does not work as the run.sh script runs check_eggs.py and re-installs the egg. Is there a file that stores the required eggs or a way to stop galaxy searching for this egg? Help would be appreciated. Thanks Shaun Webb -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.
SHAUN WEBB wrote:
Hi,
I have recently updated our galaxy install running on a cluster with the latest changesets. A new python egg was added: pysam-0.1.1-py2.4-linux-x86_64.egg.
This egg requires glib to be upgraded to GLIBC_2.7, and galaxy will not start without it. Due to constraints on our cluster we are not allowed to update glib above version 2.5.
I have rolled back the update to try to get Galaxy running but now I need to remove this python egg. Simply deleting does not work as the run.sh script runs check_eggs.py and re-installs the egg.
Is there a file that stores the required eggs or a way to stop galaxy searching for this egg?
Hi Shaun, If the egg is listed in eggs.ini, it will be searched for. You can remove it from there and will only encounter source control conflicts if we update the pysam version again. In the meantime, I'll have to find us a machine with an older glibc for us to compile eggs on. Thanks for reporting this, --nate
Help would be appreciated.
Thanks Shaun Webb
participants (4)
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Assaf Gordon -
James Taylor -
Nate Coraor -
SHAUN WEBB