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GBrowse: Difference between revisions
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== Introduction == | == Introduction == | ||
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 has been installed on cedar and the way we | 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 has been installed on cedar and the way we set it up is slightly different. Here we explain briefly how we setup Gbrowse on cedar. For more information about Gbrowse in general and how it works please take a look at Gbrowse official website: http://gmod.org/wiki/GBrowse | ||
==Gbrowse Installation== | ==Gbrowse Installation== | ||
We have installed GBrowse on a server which has access to /home and /project directories of cedar. The server is called "cedar portal" and its web address is "https://gateway.cedar.computecanada.ca". On this server we have installed apache-2.4.6 web server with apache itk module. In order to be able to access files and directories of the the users while maintaining the security each research group who is interested to have GBrowse | We have installed GBrowse on a server which has access to /home and /project directories of cedar. The server is called "cedar portal" and its web address is "https://gateway.cedar.computecanada.ca". On this server we have installed apache-2.4.6 web server with apache itk module. In order to be able to access files and directories of the the users while maintaining the security, we create a shared-account for each research group who is interested to have a GBrowse account. The itk module is used to assign uid of the shared-account for any member of the corresponding group who is successfully login to cedar portal. The user name and password are the same as the user name and password for any computecanada system. Each shared-account has its own GBowse instance. Therefore, every GBrowse instance act as a user with uid of that shared-account correspond to that group. In this way GBrowse is able to read files of users withing a research group. Please note that as GBrowse (shared-account) can read your GBrowse config files, any other member of your group can also read those particular config files. If you agree with that and If you need GBrowse on cedar portal please send a request to support@computecanada.ca | ||
==GBrowse Setup== | ==GBrowse Setup== | ||
===Gbrowse Config Files=== | ===Gbrowse Config Files=== | ||
Since Gbrowse needs to be able to read config files of all users within a group, the config files for each group are installed in /project and on following directories: | Since Gbrowse needs to be able to read config files of all users within a group, the config files for each group are installed by the admin in /project and on following directories: | ||
/project/GROUPID/gbrowse/USERNAME/conf | /project/GROUPID/gbrowse/USERNAME/conf | ||
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GBrowse is able to read .bam files directly, e.g., you do not need to upload them to the database in order to display them. If you want GBrowse to read these kind files you need to pay attention to following: | GBrowse is able to read .bam files directly, e.g., you do not need to upload them to the database in order to display them. If you want GBrowse to read these kind files you need to pay attention to following: | ||
* Files need to be copied to your /project directory and they should be readable for group. | * Files need to be copied to your /project directory and they should be readable for group. | ||
* the directory that contains files and also all top directories should be readable by the group, e.g., the group mode of the group directories should have SGID bit (Set Group ID up on execution) with small "s" (not | * the directory that contains files and also all top directories should be readable by the group, e.g., the group mode of the group directories should have SGID bit (Set Group ID up on execution) with small "s" (not "S"). | ||
* make sure that your file's group in project directory is set to your group membership and not your username. | * make sure that your file's group in project directory is set to your group membership and not your username. | ||
* Edit your conf file to specify the path to the bam file. Here is an example | * Edit your conf file to specify the path to the bam file. Here is an example | ||
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===Setup Database=== | ===Setup Database=== | ||
Before using GBrowse | Before using GBrowse, you need to ask for an database account. Please send your request to support@computecanada.ca regarding a database account on cedar. Then you need to setup their own database. More information about setting up database on computecanada is here. | ||
If you use MySQL, in order to make a MySQL connection from GBrowse you need to use the following setup in your corresponding GBrowse config files | |||
[username_example_genome:database] | [username_example_genome:database] | ||
db_adaptor | db_adaptor = Bio::DB::SeqFeature::Store | ||
db_args = | db_args = -adaptor DBI::mysql | ||
-dsn DATABASE;mysql_read_default_file= | -dsn DATABASE;mysql_read_default_file=~/.my.cnf | ||
-user SHARED | -user SHARED | ||
where | where DATABASE is the name of your database. The .my.cnf file is a text file that is created by the administrator and it contains all information that is required for the shared-account to make a MySQL connection to MySQL. | ||
If you decide to | If you decide to use Postgres you need to use the following setup in your corresponding GBrowse config files | ||
[username_example_genome:database] | |||
db_adaptor = Bio::DB::SeqFeature::Store | |||
db_args = -adaptor -adaptor DBI::Pg | |||
-dsn = dbi:Pg:dbname=DATABASE | |||
where DATABASE is the name of your database. | |||
===Upload Files to Database=== | ===Upload Files to Database=== | ||