User: ali

gravatar for ali
ali20
Reputation:
20
Status:
New User
Location:
Canada
Last seen:
3 years, 3 months ago
Joined:
3 years, 7 months ago
Email:
a**@yusuf.email

Posts by ali

<prev • 15 results • page 1 of 2 • next >
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Comment: C: Galaxy Upload Tool - Genome Version
... nopes, in the question i stated `upload.py`. ...
written 3.3 years ago by ali20
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Comment: C: Galaxy Upload Tool - Genome Version
... alright, but that is for when defining in the tool XML. when I'm looking at `upload.py`, which variable has the $dbkey stored? For example, dataset.ext has the file extension stored, and output_path has the full path stored. I'm trying to modify the upload tool to run  a script on certain types of f ...
written 3.3 years ago by ali20
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Comment: C: Galaxy Upload Tool - Genome Version
... alright, but which variable stores the genome version if specified ...
written 3.3 years ago by ali20
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Galaxy Upload Tool - Genome Version
... In the upload tool, upload.py, is it possible to determine which genome the user had selected (or the version if it can automatically determine) specifically this code block `def __main__():` ...
python galaxy genome upload written 3.3 years ago by ali20 • updated 3.3 years ago by jmchilton1.0k
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Comment: C: Accessing files created from the history
... when iterating over the name, how can I get the filename? or the attribute:name Im using ${f.metadata.name} but this does not work   ...
written 3.6 years ago by ali20
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Comment: C: Accessing files created from the history
... I dont see anything in the documentation relating to using hda or something similar as a method to get the path of the file on the local disk. I'm reading this from the documentation on param type='data' which i think might work. The following will find all "coordinate interval files" contained wit ...
written 3.6 years ago by ali20
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Accessing files created from the history
... I would like to write a tool that will get the abs path, or relative path to the galaxy folder of the files created/added/imported in the user's history How can i do that? I'm reading a ton of documentation, but most of it points to manipulating datasets in the galaxy interface, which is not what i ...
datasets tools galaxy tool written 3.6 years ago by ali20 • updated 3.6 years ago by jmchilton1.0k
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Comment: C: Toolshed tools, create tool data file on installation
... yes, i mean .loc files ...
written 3.6 years ago by ali20
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Toolshed tools, create tool data file on installation
... How can I setup my custom tool on our local running version of the toolshed to automatically create a configuration file in the $__tool_data_path__ directory?   The file does not need to have data in it, i just need to know how to include this in the installation procedure ...
tools galaxy toolshed written 3.6 years ago by ali20 • updated 3.6 years ago by Bjoern Gruening5.0k
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Comment: C: Limiting User Access to specific Tools
... if the tool calls upon a script using the <command> tag are there env variables that are present that can reveal to me the user that is logged in? ...
written 3.6 years ago by ali20

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