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GBrowse: Difference between revisions
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In order for GBrowse to be able to access your files and directories, our staff will create a shared account for each research group that requests access to GBrowse. While using GBrowse, any member of a research group can read GBrowse config files and input files belonging to any other member of that group. If you wish to use GBrowse, the Principal Investigator (PI) of your group must agree to this change from the usual file security practices. Have the PI write to our [[ | In order for GBrowse to be able to access your files and directories, our staff will create a shared account for each research group that requests access to GBrowse. While using GBrowse, any member of a research group can read GBrowse config files and input files belonging to any other member of that group. If you wish to use GBrowse, the Principal Investigator (PI) of your group must agree to this change from the usual file security practices. Have the PI write to our [[technical support]] indicating that they want a GBrowse account to be created for the group, and that they understand the implications of a shared account. | ||
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GBrowse is able to read | GBrowse is able to read .bam files directly. You do not need to upload them to the database in order to display them. If you want GBrowse to read these .bam files directly: | ||
* Files need to be copied to your <code>/project</code> directory and they should be readable by the group. | * Files need to be copied to your <code>/project</code> directory and they should be readable by the group. | ||
* The directory that contains the | * The directory that contains the .bam files must have the <tt>setgid</tt> and <tt>group-execute</tt> bits turned on; that is, the output of <code>ls –l</code> must show a small "s" in the group-execute field (not a large "S"). | ||
* Make sure that the .bam file's group ownership is set to your group and not to your username. For example, <code>jsmith:jsmith</code> is wrong, <code>jsmith:def-kjones</code> is right. | * Make sure that the .bam file's group ownership is set to your group and not to your username. For example, <code>jsmith:jsmith</code> is wrong, <code>jsmith:def-kjones</code> is right. | ||
* Edit your config file to specify the path to the .bam file. Here is an example: | * Edit your config file to specify the path to the .bam file. Here is an example: | ||