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Key question (FIXME)Objectives
First learning objective. (FIXME)
Download and unpack databases
tar -xvf databases.tar.gz
Inside the unpacked “databases” directory you will find three files: Reference_DB.fas and gb203_pr2_all_10_28_97p_noorg.fasta, and tax_d.bin. These files are used for filtering results within eukref_gbretrieve.py. All three files must be in the current working directory where you run the eukref_gbrtrieve.py script in Step 6.
Get GenBank nt database
Locate a copy of GenBank nt database in use at your institution or on your server. At the EukRef workshop there is a copy on the Amazon server. GenBank NT should ideally be downloaded to a server. There will be more than 40 files totaling more than 30 GB. Downloading can take several hours. You may wish to install and use a tool like wget. In a workshop setting download one time and allow access for all participants.
Make a new folder called DATABASEFOLDER. From ftp://ftp.ncbi.nlm.nih.gov/blast/db/ download taxdb.tar.gz and all nt.tar.gz files. Also, download all nt_.tar.gz.md5 files.
Unpack with the following command:
for i in nt*; do tar -xvf $i ; done
Run md5 checksum to ensure all files are fully downloaded.
(NOTE: Add explanation of what checksums are and instructions on how to run.)
Before running the pipeline run the following commands
(you can also add BLASTDB to your PATH permanently)
(NOTE - Add instructions on how to modify PATH.)
First key point. Brief Answer to questions. (FIXME)