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GBrowse: Difference between revisions
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GBrowse is a combination of database and interactive web pages for manipulating and displaying annotations on genomes. It requires a web interface to display. GBrowse | GBrowse is a combination of database and interactive web pages for manipulating and displaying annotations on genomes. It requires a web interface to display. GBrowse is installed on [[Cedar]]. The web address of the installation is https://gateway.cedar.computecanada.ca. | ||
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In order for GBrowse to be able to access your files and directories, | 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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Since | Since GBrowse needs to be able to read config files of all users within a group, place your GBrowse config files in the following directory: | ||
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where <code>''DATABASE''</code> is the name of your database and <code>''SHARED''</code> is the shared | where <code>''DATABASE''</code> is the name of your database and <code>''SHARED''</code> is the shared account. The <code>.my.cnf</code> file is a text file that is created by our staff. It contains information required for the shared account to make a connection to MySQL. | ||
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If you decide to use Postgres you need the following in your GBrowse config files: | If you decide to use Postgres, you need the following in your GBrowse config files: | ||
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GBrowse is able to read <code>.bam</code> 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: | GBrowse is able to read <code>.bam</code> 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 <code>.bam</code> files must have the setgid and group-execute bits turned on; that is, the output of <code>ls –l</code> must show a small "s" in the group-execute field (not large "S"). | * The directory that contains the <code>.bam</code> 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 | * 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 | * Edit your config file to specify the path to the .bam file. Here is an example: | ||
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In this example <code>''DATABASE''</code> is the name of your database and <code>example_genomic_sequence.fa</code> is the [https://en.wikipedia.org/wiki/FASTA_format | In this example <code>''DATABASE''</code> is the name of your database and <code>example_genomic_sequence.fa</code> is the [https://en.wikipedia.org/wiki/FASTA_format FASTA file] containing the entire genome that you want to visualize with GBrowse. <code>header_file</code> contains details about the length of the chromosomes. Here is an example of a header file: | ||
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Once you uploaded your data to your database you need to grant view access to the <code>''SHARED''</code> account so that GBrowse is able to access your database for reading. Please see [[Database servers#How_to_share_your_MySQL_data|How to share your MySQL data]]. | Once you uploaded your data to your database, you need to grant view access to the <code>''SHARED''</code> account so that GBrowse is able to access your database for reading. Please see [[Database servers#How_to_share_your_MySQL_data|How to share your MySQL data]]. | ||
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