Changeset 1292:160bc7278171

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Timestamp:
05/12/08 14:55:48 (8 months ago)
Author:
Greg Von Kuster <greg@bx.psu.edu>
branch:
default
convert_revision:
svn:9bcadc22-80f8-0310-8a53-c8f022958886/galaxy/trunk@2653
Message:

Added code for integration with C. Elegans / GBrowse test server.

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  • lib/galaxy/web/controllers/tool_runner.py

    r1166 r1292  
    1919    @web.expose 
    2020    def biomart(self, trans, tool_id='biomart', **kwd): 
     21        """Catches the tool id and redirects as needed""" 
     22        return self.index(trans, tool_id=tool_id, **kwd) 
     23 
     24    @web.expose 
     25    def gbrowse_elegans(self, trans, tool_id='gbrowse_elegans', **kwd): 
    2126        """Catches the tool id and redirects as needed""" 
    2227        return self.index(trans, tool_id=tool_id, **kwd) 

  • static/gbrowse/gbrowse_build_sites.txt

    r365 r1292  
    22# TODO: Uncomment the 1st lines and eliminate the 2nd test lines when the prototype is completed. 
    33#wormbase       http://gvk.bx.psu.edu/cgi-bin/gbrowse/volvox?   briggsae,briggsae_cb25,brugia,elegans,elegans_gmap,elegans_pmap,fly,fly31,nGASP,nGASP_submissions,remanei,wormbase,ws77,yeast_chr1 
    4 wormbase      http://gvk.bx.psu.edu/cgi-bin/gbrowse/volvox?   ctgA,tmpfiller1,tmpfiller2 
     4# 2nd test line: wormbase     http://gvk.bx.psu.edu/cgi-bin/gbrowse/volvox?   ctgA,tmpfiller1,tmpfiller2 
    55#Harvested from http://flybase.bio.indiana.edu/cgi-bin/gbrowse/dmel/ 
    66#flybase        http://flybase.bio.indiana.edu/cgi-bin/gbrowse/dmel/    dana,dere,dgri,dmel,dmoj,dper,dpse,dsec,dsim,dvir,dwil,dyak,dmelstocks 
    7 flybase http://flybase.bio.indiana.edu/cgi-bin/gbrowse/dmel/    tmpfiller1,tmpfiller2 
     7# 2nd test line: flybase        http://flybase.bio.indiana.edu/cgi-bin/gbrowse/dmel/    tmpfiller1,tmpfiller2 
     8elegans http://brie3.cshl.edu:9000/cgi-bin/gbrowse/elegans/     brugia,briggsae_cb25,briggsae,elegans,wormbase,elegans_gmap,elegans_pmap,nGASP,ws77,remanei,mouse,nGASP_submissions,Gbrowse_karyotype,yeast_chr1,yeast_chr1 

  • tool_conf.xml.sample

    r1262 r1292  
    99    <tool file="data_source/biomart.xml" /> 
    1010    <tool file="data_source/biomart_test.xml" /> 
     11    <tool file="data_source/gbrowse_elegans.xml" /> 
    1112    <tool file="data_source/encode_db.xml" /> 
    1213    <tool file="data_source/hbvar.xml" />  

  • universe_wsgi.ini.sample

    r1213 r1292  
    9393# Comma separated list of UCSC / gbrowse browsers to use for viewing 
    9494ucsc_display_sites = main,test,archaea 
    95 gbrowse_display_sites = wormbase,flybase 
     95gbrowse_display_sites = wormbase,flybase,elegans 
    9696 
    9797# Serving static files (needed if running standalone)