GBiB: From download to BLAT at assembly hubs: Difference between revisions
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(Created page with "== GBiB installation == * Create a folder at your machine to place the installation files: $> sudo mkdir /usr/local/src/gbib == GBiB Configuration == * Click at "Setting...") |
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* Create a folder at your machine to place the installation files: | * Create a folder at your machine to place the installation files: | ||
$> sudo mkdir /usr/local/src/gbib | $> sudo mkdir /usr/local/src/gbib | ||
* Log in at UCSC Genome Browser virtual store: | |||
** [http://www.genome-store.ucsc.edu Genome Store] | |||
** Click in "Add to cart" at the box relative to GBiB. | |||
** Click in "My products" on menu. | |||
** Note the download address. | |||
** Download GBiB to /usr/local/src/gbib: | |||
$> sudo wget https://genome-store.ucsc.edu/media/products/gbib.zip | |||
Revision as of 11:11, 6 May 2015
GBiB installation
- Create a folder at your machine to place the installation files:
$> sudo mkdir /usr/local/src/gbib
- Log in at UCSC Genome Browser virtual store:
- Genome Store
- Click in "Add to cart" at the box relative to GBiB.
- Click in "My products" on menu.
- Note the download address.
- Download GBiB to /usr/local/src/gbib:
$> sudo wget https://genome-store.ucsc.edu/media/products/gbib.zip
GBiB Configuration
- Click at "Settings".
Assembly hub configuration
- Log in again using ssh:
$> ssh browser@localhost -p 1235
Track hub configuration
- Create the contents of trackDb.txt:
$> sudo cat > /usr/local/share/gbib/hubs/geneNetwork/schMan2/trackDb.txt << EOI
track SMPs
EOI
Blat configuration
- From the folder that contains the .2bit file, start two gfServer's, specifying the assembly hub ports that will be used to access the DNA sequence and the aminoacids sequence:
$> gfServer start 127.0.0.1 42422 -stepSize=5 schMan2.2bit &
$> gfServer start 127.0.0.1 42423 -trans schMan2.2bit &
Custom track configuration
track type=bigBed
GBiB maintenance
- Make an update of all softwares and data:
$> gbibOnline
