Building Python Eggsfor Galaxy With Python-2.6

Question: Building Python Eggsfor Galaxy With Python-2.6

9.5 years ago by

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

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modified 9.5 years ago • written 9.5 years ago by Amit Kr.. Mandal • 20

9.5 years ago by

Greg Von Kuster • 840

Greg Von Kuster • 840 wrote:

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

ADD COMMENT • link written 9.5 years ago by Greg Von Kuster • 840

9.5 years ago by

Amit Kr.. Mandal • 20

Amit Kr.. Mandal • 20 wrote:

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 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

ADD COMMENT • link written 9.5 years ago by Amit Kr.. Mandal • 20

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