Thanks for the example, Frank.
You can upload to data libraries directly from the local filesystem. The
relevant documentation is here:
http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files
Eli, with respect to the question about modifying galaxy-dist/lib:
Unfortunately, there's not much in the way of documentation for developing the
Galaxy application/framework itself. The code is commented to some degree. If
you have a specific question or problem you're trying to solve we can probably
point you in the right direction.
--nate
On Apr 16, 2012, at 8:54 AM, Frank Sørensen wrote:
> Hi Eli,
>
> That could easily be accomplished without changing the code, by writing a
> simple tool.
>
> The xml-file:
>
> <tool id="importer" name="Import" version="0.0.1" hidden="false">
> <description>Import files</description>
> <parallelism method="basic"></parallelism>
> <command interpreter="python">
> importer.py
> -$link "$infile" "$outfile"
> </command>
> <inputs>
> <param type="text" name="infile" size="180" label="Enter path to file to
> upload" />
> <param name="link" type="boolean" truevalue="--link" checked="false"
> falsevalue="" label="Link to file" help="Should the file be linked instead of
> copied into Galaxy?" />
> </inputs>
> <outputs>
> <data format="data" name="outfile" label="Imported file" />
> </outputs>
> <help>
>
> **What it does**
>
> This tool is a simple file importer
>
> ------
>
> The path string points to a local file, that should be imported into the
> current history.
>
> </help>
> </tool>
>
>
> And the Python script:
>
> #!/usr/bin/python
>
> import argparse, os
> version = '0.0.1'
> progName='importer'
>
>
> def __main__():
> parser = argparse.ArgumentParser(
> prog=progName,
> description='Simple Galaxy file importer')
>
> parser.add_argument('--version', action='version',
> version='%(prog)s '+version,
> help='Display version information')
>
> parser.add_argument('infile', nargs=1,
> type=str,
> help='input filename mask')
>
> parser.add_argument('savefile', nargs=1,
> type=str,
> help='savefile filename')
>
> parser.add_argument('-l','--link',
> action='store_true',
> default=False,
> help='Make symbolic link to file')
>
>
> try:
> args = parser.parse_args()
>
> if args.link:
> os.system('ln -fs %s %s' % (args.infile[0],args.savefile[0]))
> else:
> os.system('cp %s %s' % (args.infile[0],args.savefile[0]))
>
>
> except Exception as E:
> print >> sys.stderr, E
> exit(1)
> pass
>
> if __name__=="__main__": __main__()
>
>
> I have written a handful of Galaxy tools that implements this technique, and
> it works like a charm. However this specific example is copy and pasted and
> simplified from one of my existing tools, so I haven't actually tried it, so
> It might contain a few spelling mistooks.
>
> With a minimum of coding, the opposite can also be implemented, namely
> exporting files from galaxy to an external local file.
>
> Kind regards
>
> Frank Sorensen
>
> Den 16-04-2012 08:13, Eli Reuveni skrev:
>> Hi,
>> I have a local galaxy instance in my institute and have few basic questions:
>>
>> 1) I need to enable galaxy to upload large files from the local galaxy
>> server without the need to use the ftp or the file upload module, is there
>> an easy way to do it or do I need to write a special code?
>> 2) I need to customize galaxy Python code (i.e., under the
>> ~/galaxy-dist/lib directory). Where can I find documentation of the galaxy
>> Python classes (using wiki or other format)
>>
>> Thanks in advanced,
>>
>
> --
> Frank Sørensen, B.Sc., Programmer
> Molecular Diagnostic Laboratory (MDL)
> Molekylær Medicinsk Afdeling (MOMA)
> Århus Universitetshospital Skejby, Brendstrupgårdsvej, 8200 Århus N
> Tlf. +45 7845 5363
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