On May 22, 2010, at 3:28 AM, Edward Kirton wrote:

Hi Davide,

I'm trying to get this working too but applying your patch gives me an error

Nevermind, I think galaxy team should work on this :-)

Even if you had the patch working you may get some errors when a tool tries to read the config file. Apparently this is defined somewhere else too... I've been trying to import some data from UCSC and this is what I've got (after my patch):

Traceback (most recent call last):

File "/data/galaxy_dist/tools/data_source/data_source.py", line 6, in

from galaxy.util import gzip_magic

File "/data/galaxy_dist/lib/galaxy/util/__init__.py", line 21, in

pkg_resources.require( 'docutils' )

File "/data/galaxy_dist/lib/galaxy/eggs/__init__.py", line 337, in require

c = Crate()

File "/data/galaxy_dist/lib/galaxy/eggs/__init__.py", line 197, in __init__

self.galaxy_config = GalaxyConfig()

File "/data/galaxy_dist/lib/galaxy/eggs/__init__.py", line 299, in __init__

raise Exception( "error: unable to read Galaxy config from %s" % GalaxyConfig.config_file )

Exception: error: unable to read Galaxy config from /data/galaxy_dist/0

As you can see the config file name is passed here as "0", that means that the tool is reading it somewhere where is not defined (or it should be defined as universe_wsgi.ini)...

I'll ask the audience :-)

Traceback (most recent call last):
File "./scripts/check_eggs.py", line 20, in <module>
    from galaxy.eggs import Crate
File "/house/tooldirs/galaxy/galaxy-jgi/lib/galaxy/eggs/__init__.py", line 290, in <module>
    class GalaxyConfig( object ):
File "/house/tooldirs/galaxy/galaxy-jgi/lib/galaxy/eggs/__init__.py", line 291, in GalaxyConfig
    config_file = os.path.join( galaxy_dir, sys.argv[2] )
IndexError: list index out of range
Some eggs are out of date, attempting to fetch...
Traceback (most recent call last):
File "./scripts/fetch_eggs.py", line 21, in <module>
    from galaxy.eggs import Crate, EggNotFetchable
File "/house/tooldirs/galaxy/galaxy-jgi/lib/galaxy/eggs/__init__.py", line 290, in <module>
    class GalaxyConfig( object ):
File "/house/tooldirs/galaxy/galaxy-jgi/lib/galaxy/eggs/__init__.py", line 291, in GalaxyConfig
    config_file = os.path.join( galaxy_dir, sys.argv[2] )
IndexError: list index out of range
Fetch failed.

I've got IT coming by to help me next week; I'll be sure to pass-along anything I learn.

Cheers!
Ed

On Fri, May 21, 2010 at 1:32 AM, Davide Cittaro <davide.cittaro@ifom-ieo-campus.it> wrote:

On May 21, 2010, at 10:13 AM, Davide Cittaro wrote:

I'm now looking where and how the config file is passed to galaxy from command line...

It works after this:

$ hg diff lib/galaxy/eggs/__init__.py
diff -r 48432330228e lib/galaxy/eggs/__init__.py
--- a/lib/galaxy/eggs/__init__.py Fri May 14 10:37:36 2010 -0400

+++ b/lib/galaxy/eggs/__init__.py Fri May 21 10:30:59 2010 +0200
@@ -288,7 +288,7 @@
   raise EggNotFetchable( missing )

class GalaxyConfig( object ):

- config_file = os.path.join( galaxy_dir, "universe_wsgi.ini" )
+ config_file = os.path.join( galaxy_dir, sys.argv[2] )
   always_conditional = ( 'GeneTrack', 'pysam' )

   def __init__( self ):
   self.config = ConfigParser.ConfigParser()

Of course, this assumes that the config file is always the second argument (which is seems mandatory to me...)

d

/*
Davide Cittaro

Cogentech - Consortium for Genomic Technologies
via adamello, 16
20139 Milano
Italy

tel.: +39(02)574303007
e-mail: davide.cittaro@ifom-ieo-campus.it
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