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fhcrc / taxtastic

Create and maintain phylogenetic "reference packages" of biological sequences.
GNU General Public License v3.0
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use local copy of ncbi taxdump #79

Closed kbseah closed 7 years ago

kbseah commented 8 years ago

Hello - I'm using taxtastic because I'm interested in using pplacer to classify short reads against a reference. Is it possible to use a local copy of the NCBI taxdump, instead of downloading it new to make the Sqlite taxonomy database?

crosenth commented 8 years ago

Hi Brandon,

If a file named taxdump.zip exists in your --download-dir then it will not be re-downloaded.

For flexibility, I have pushed two new switches to master (taxit new_database --taxdump-file and `taxit new_database --taxdump-url``) that will be included in the next release (v0.5.6).

Chris

kbseah commented 8 years ago

Hello Chris, Thanks for the quick reply! I will give it a try. -- Brandon On Feb 5, 2016 11:43 PM, "Chris Rosenthal" notifications@github.com wrote:

Hi Brandon,

If a file named taxdump.zip exists in your --download-dir then it will not be re-downloaded.

For flexibility, I have pushed two new switches to master (taxit new_database --taxdump-file and taxit new_database --taxdump-url`) that will be included in the next release (v0.5.6).

Chris

— Reply to this email directly or view it on GitHub https://github.com/fhcrc/taxtastic/issues/79#issuecomment-180606850.