IGV Integration

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Setting up

       NOTE : You need to have mod_xsendfile (apache module : https://tn123.org/mod_xsendfile/
        wget https://tn123.org/mod_xsendfile/
        tar -xvzf mod_xsendfile-0.12.tar.gz
        yum install httpd-devel (si nécessaire)
        apxs -cia mod_xsendfile.c
        1. If not done already, edit galaxy apache configuration file and add those lines in location bloc
            <Location "/">
                # ....
                #  other apache directive
                # .....
                XSendFile on
                XSendFilePath /
            This should be added to the existing <Location "/"> block if you already have one, and adjusted accordingly if you're serving Galaxy from a subdirectory.
            Note: If you use a version of mod_xsendfile older than 0.10, use "XSendFileAllowAbove on" instead of "XSendFilePath /"

        2. Setup IGV as a Display Application in Galaxy. Add the following to the bam datatype in datatypes_conf.xml file:
            <display file="igv/bam.xml" />
        This is done already in the new code ...
        3. Setup Apache to allow unauthenticated access to the bam files. This is a small security hole, but is necessary since IGV
        cannot authenticate to Galaxy. To do this I adding the following LoctionMatch section to the httpd.conf file.

            <LocationMatch ^/display_application/[a-zA-Z0-9]+/igv.*>
                    RequestHeader set REMOTE_USER igv_display@example.org
                    Satisfy Any
                    Order deny,allow
                    Allow from all

        4. set apache_xsendfile = True in the [app:main] section of universe_wsgi.ini and restart Galaxy.
        5. Restart apache server

Add a custom genome file to igv and galaxy

        1. Open IGV and add your genome with 'Genomes > Create .genome file'. It is very important to remember the 'uniq identifier'
        2. Edit the file galaxy-dist/tool-data/shared/igv/igv_build_sites.txt and add the uniq_identifier to the list of dbkey and ivg_build_name
           for both 'web_link_main' and 'local_default'.
           For example if your uniq_identifier is 'contigs', the file becomes like this
           #site_id    site_name    site_url    dbkey    ivg_build_name
           web_link_main    web current    http://www.broadinstitute.org/igv/projects/current/igv.php    hg19,hg_g1k_v37,hg18,....,ppatens_1.2,D.discoideum,contigs   
           local_default    local    http://localhost:60151/load    hg19,hg_g1k_v37,hg18,....,ppatens_1.2,D.discoideum,contigs    hg19,b37,hg18,...,ppatens_1.2,D.discoideum,contigs

           NOTE : the line starting with 'web_link_main ...' will allow you to use the web version of IGV
           NOTE : the line starting with 'local_default ...' will allow you to use a local version of IGV

        3. Edit the file galaxy-dist/tool-data/shared/ucsc/builds.txt and add a new line with the uniq_identifier and a description.
           For example if your uniq_identifier is 'contigs', the new line can be :
           contigs    Contigs not in public (contigs)
        4. Restart Galaxy


Using igv with your genome

       1. Upload or reate a BAM file. Be carefull that the genome you've used must be the same as the one you've added to IGV in the
           previous step !!!!
        2. Edit the property of the bam dataset (click on the pencil) and change the Database/Build to the one you've added in the previous
            steps. A new link with 'display with IGV web current local' will show up in the dataset box.
        3. If you chose the local option, be sure to have IGV alreaedy running localy.
           If you chose the web current option, you must open it with the Java Web Start program (which should be in /usr/bin/javaws)

By Ibouniyamine Nabihoudine (INRA - Sigenae - Toulouse)

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