Hello Amit,
The problematic GeneTrack egg and dependent eggs have been eliminated
from eggs.ini in change set 2417, which is available for download, so
this issue should be resolved if you get the latest build. Please let
mek now if you still encounter problems. We are planning to eliminate
the GeneTrack tool soon from the distribution.
Thanks for you message Amit,
Greg Von Kuster
Galaxy Development Team
Amit Kr.. Mandal wrote:
Hello all,
I'm interested in adding tools and some long drawn jobs and hence
trying to locally install Galaxy. My system is an Ubuntu 9.04 [Linux
2.6.28-11-generic; i686] with python 2.6.2.
As such I have to build the eggs using "scramble.py". All the eggs
successfully build except the 'GeneTrack' egg
(
http://genetrack.googlecode.com/files/GeneTrack-1.0.3.zip).
The console output says -
scramble(): Beginning build
Traceback (most recent call last):
File "scramble.py", line 39, in <module>
execfile( "setup.py", globals(), locals() )
IOError: [Errno 2] No such file or directory: 'setup.py'
scramble(): Egg build failed for GeneTrack-1.0.3
I've attached a txt file with the detailed console output. Is the
version of GeneTrack being downloaded wrong as per the Galaxy
distribution (I've used mercurial to get the latest). Kindly help.
This would be too much to ask, but if anyone has compiled the egg on
the same configuration, please share. It would be of great help!
thanks and regards,
Amit Kumar Mandal
Graduate Student
Genomics & Molecular Medicine
IGIB, Delhi
------------------------------------------------------------------------
amitm@megh:~/galaxy_dist$ sudo sh setup.sh
Not overwriting existing datatypes_conf.xml
Not overwriting existing reports_wsgi.ini
Not overwriting existing tool_conf.xml
Not overwriting existing universe_wsgi.ini
Not overwriting existing tool-data/alignseq.loc
Not overwriting existing tool-data/binned_scores.loc
Not overwriting existing tool-data/blastdb.loc
Not overwriting existing tool-data/encode_datasets.loc
Not overwriting existing tool-data/liftOver.loc
Not overwriting existing tool-data/maf_index.loc
Not overwriting existing tool-data/maf_pairwise.loc
Not overwriting existing tool-data/microbial_data.loc
Not overwriting existing tool-data/phastOdds.loc
Not overwriting existing tool-data/quality_scores.loc
Not overwriting existing tool-data/regions.loc
Not overwriting existing tool-data/twobit.loc
One of the python eggs necessary to run Galaxy couldn't be downloaded
automatically. You may want to try building it by hand with:
python scripts/scramble.py GeneTrack
amitm@megh:~/galaxy_dist$ sudo python scripts/scramble.py GeneTrack
fetch_source(): Attempting to download
http://genetrack.googlecode.com/files/GeneTrack-1.0.3.zip
fetch_source(): Fetched
http://genetrack.googlecode.com/files/GeneTrack-1.0.3.zip
fetch_source(): Attempting to download
http://dalchemy.com/opensource/formkit/FormKit_0.9b2.tar.gz
fetch_source(): Fetched
http://dalchemy.com/opensource/formkit/FormKit_0.9b2.tar.gz
unpack_source(): Unpacked to:
/home/amitm/galaxy_dist/scripts/scramble/build/py2.6-noplatform/GeneTrack
scramble(): Using build script
/home/amitm/galaxy_dist/scripts/scramble/scripts/generic.py
scramble(): Beginning build
Traceback (most recent call last):
File "scramble.py", line 39, in <module>
execfile( "setup.py", globals(), locals() )
IOError: [Errno 2] No such file or directory: 'setup.py'
scramble(): Egg build failed for GeneTrack-1.0.3
amitm@megh:~/galaxy_dist$
------------------------------------------------------------------------
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