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DaehwanKimLab / centrifuge

Classifier for metagenomic sequences
GNU General Public License v3.0
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Add dependencies to README and MANUAL #193

Open alanorth opened 4 years ago

alanorth commented 4 years ago

While attempting to build the indexes using the included make targets I found out that it is expected that BLAST, Jellyfish, and nucmer (from the MUmer package) are available in the user's environment. It would save time if you specified that these are required (and which versions).

For reference, I am using centrifuge v1.0.4-beta, which was released in 2018, so I'm attempting to use versions of these other packages from around that time:

Edit: Also, are these only required to make the indexes during setup, or also during run time? Thanks!

fanninpm commented 3 years ago

As far as I can tell, BLAST, Jellyfish and MUMmer are only required to make the indices during setup. I didn't need them when I was working with a pre-built database.

josemunozc commented 1 year ago

Thanks, I hit the same issue when building the indices. Also vote for adding these details to the main instructions.