January 2009 - galaxy-user - lists.galaxyproject.org

displaying ucsc tracks when using external auth
by James Casbon 12 Jan '09

12 Jan '09

Hi All, When attempting to display a custom track on the UCSC genome browser, galaxy generates a URL such as... http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&position=chr1:1-1000&hgt.cu… The first problem I have is that the base url is wrong for the customText - I am using https - is there a way to set that? The customText parameter is the bit that allows UCSC to pick up the data - but it is not going to get past the external auth. Is there a reasonable way to fix this? I suppose there must be a way to bypass the auth if the request comes from UCSC and looks like a certain URL, but is there a better way? thanks, James

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Local Mirror *away* from server root
by Suraj Mukatira 08 Jan '09

08 Jan '09

Hi, I modified the universe_wsgi.ini file as below, based on the FAQ input # ---- HTTP Server ---------------------------------------------------------- [server:main] use = egg:Paste#http port = 8080 host = 127.0.0.1 use_threadpool = true threadpool_workers = 10 # ---- Galaxy Web Interface ------------------------------------------------- #[app:main] [composite:main] use=egg:Paste#urlmap[[BR]] /galaxy/=galaxy [app:galaxy] # Specifies the factory for the universe WSGI application paste.app_factory = galaxy.web.buildapp:app_factory log_level = DEBUG ...rest same However I get the following error: LookupError: Entry point 'urlmap[[BR]] /galaxy/=galaxy' not found in egg 'Paste' (dir: /var/www/html/galaxy_dist/eggs/py2.5-noplatform/Paste-1.5.1-py2.5.egg; protocols: paste.app_factory, paste.composite_factory, paste.composit_factory; entry_points: ) What is wrong with my modification of universe_wsgi.ini Thanks in anticiaption Sm

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bitset problem
by Jose Jorge Galan 02 Jan '09

02 Jan '09

Dear all, I am trying to intersect overlapping pieces of intervals from two queries. When the process finishes I get the following message: "Info: Skipped 2 invalid lines of 1st dataset, 1st line #39: "chrX 153771797 154493114 ", problem: 536870912 is larger than the size of this BitSet (536870912)." How can I solve this problem? I have tried to do the same intersect with the two queries in BED and in interval format, but the results are the same. Thanks in advance, Yours, Jose Jorge Galan, PhD _________________________________________________________________ Invite your mail contacts to join your friends list with Windows Live Spaces. It's easy! http://spaces.live.com/spacesapi.aspx?wx_action=create&wx_url=/friends.aspx…

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