![]() Running bin/ also sets up the "DNA" track. The first script to run is bin/ that script is the way you tell JBrowse about what your reference sequences are. "db_adaptor": "Bio::DB::SeqFeature::Store", "description": "GMOD Summer School 2013 P. There are adaptors available for use with many other databases, such as Chado and Bio::DB::GFF. Here, we'll use the Bio::DB::SeqFeature::Store adaptor in "memory" mode to read a directory of files. There are four basic steps to setting up an instance of JBrowse: ![]() You should see a "Congratulations" page. run setup.sh to configure this copy of JBrowse.Wget unzip GMOD_Summer_School_2013_JBrowse.zip cd GMOD_Summer_School_2013_JBrowse/ unzip JBrowse-1.9.8.zip mv JBrowse-1.9.8 jbrowse download the demo bundle from and unzip it.JBrowse presentation Setting up JBrowse Getting JBrowseĬd /var/www sudo mkdir jbrowse_demo sudo chown ubuntu.ubuntu jbrowse_demo cd jbrowse_demo How and why JBrowse is different from most other web-based genome browsers, including GBrowse. It's also very useful to know how to tab-complete in the shell. Make sure you can copy/paste from the wiki. Sudo apt-get install libpng12-0 libpng12-dev build-essential libncurses5-dev This is how they were installed: (don't do this yourself) Other prerequisites are installed by JBrowse automatically. samtools, and its dependency libncurses5-dev.Optional, for BAM files ( setup.sh tries to install these for you in the JBrowse directory): Optional, for generating images from Wiggle files: These have already been set up on the VM image. 4.3 Combination tracks (coming in 1.10.0).
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