InstallingGenomes

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1 Installing Genomes

Find the genome you are looking for at the clearinghouse:

http://clearinghouse.theseed.org/clearinghouse_browser.cgi

You can download to a GFF file.

Convert the GFF to a SEED skeleton with gff2seed:

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Installing a genome with precomputed data.

Given a genome directory 290398.3:

fig add_genome ./290398 

Output will look something like this:

WARNING: For /home/olson/290398.3, no rna directory/home/olson/290398.3 is O.K. 
07/13/2005 16:14:57 <main>: Building seek file. 
07/13/2005 16:14:57 <main>: Indexing contigs for /disks/space0/fig/FIGdisk.Jun17/FIG/Data/Organisms/290398.3. 
07/13/2005 16:14:58 <main>: Harvesting with index_contig_files. 
07/13/2005 16:14:58 <main>: Contig indexing complete. 
07/13/2005 16:14:59 <main>: Gathering genome data. 
07/13/2005 16:14:59 <main>: Checking /disks/space0/fig/FIGdisk.Jun17/FIG/Data/Organisms/290398.3. 
07/13/2005 16:14:59 <main>: Genome counts complete. 
07/13/2005 16:14:59 <main>: Preparing to load features. 
07/13/2005 16:14:59 <main>: Processing 290398.3. 
07/13/2005 16:14:59 <main>: Parsing alias file. 
07/13/2005 16:15:00 <main>: Features loaded. 
07/13/2005 16:15:00 <main>: Checking translation method. 
07/13/2005 16:15:00 <main>: Indexing files. 
07/13/2005 16:15:00 <main>: Indexing /disks/space0/fig/FIGdisk.Jun17/FIG/Data/Organisms/290398.3/Features/peg/fasta. 
07/13/2005 16:15:22 <main>: Translation indexing complete.Added 290398.3 

fig@brucella FIGdisk $ index_sims FIG/Data/NewSims/sims.29098.3.1 
07/13/2005 16:19:51 <main>: Indexing sims file FIG/Data/NewSims/sims.29098.3.1 (1 of 1) 
07/13/2005 16:20:02 <main>: Sim index processing complete 

assignments generated by

fig@brucella FIG $ fig pegs 290398.3 | auto_assign 
fig@brucella FIG $ fig assign_functionF master:auto_assign ~olson/290398.3.assignments 

2 Installing Metagenomes

See InstallingMetagenomes written by Rob