hello Greg, Thank you for helping out. I've now been able to compile and run Galaxy locally. I would like to share an information. The web-address for the "flup" package (needed) for compiling the concerned egg, has changed after your latest change set 2417. The add. is - "http://www.saddi.com/software/flup/dist/archive/flup-r2311.tar.gz" Kindly update this in your next change set. I tried compiling the egg by manually downloading the package and keeping it in the "galaxy_dist/scripts/scramble/archives" directory but 'setup.sh' didn't detect that. So I had to edit the 'eggs.ini' file for the correct URL. I hope that it is fine. thanks again for putting up this immensely useful tool.
regards,
Amit Kumar Mandal Graduate Student Genomics & Molecular Medicine IGIB, Delhi
-----Original Message----- From: Greg Von Kuster [mailto:ghv2@psu.edu] Sent: Wed 5/27/2009 2:10 AM To: Amit Kr.. Mandal Cc: galaxy-user@bx.psu.edu Subject: Re: [galaxy-user] building python eggsfor Galaxy with python-2.6
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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