NCBI installation updates about mitoz HOT 4 CLOSED

Dear aremkho,

This is a very good question.

I noticed this problem during the development of MitoZ. MitoZ relies on the ETE3 pakcage, which must install the NCBI taxonomy database into ~/.etetoolkit/ directory:

.etetoolkit/
├── taxa.sqlite
└── taxa.sqlite.traverse.pkl

As you can see, the ETE3 package will transform the ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz into two files: taxa.sqlite and taxa.sqlite.traverse.pkl under the ~/.etetoolkit/ directory. So the taxonomy database on your HPC
will not work for ETE3 package.

My goal was to install the database into somewhere else, then I checked the ETE3's source code, and found that I cannot do it easily, because one has to modify much of the ETE3's source code.

Since I want to make it more easily to distribute MiotZ, for example, use conda to install all relevant dependencies automatically, so I gave up on this.

NB: I am currently updating MitoZ, but the version 2.2 is still testing: the algorithm is the same as verion 1.0, changes only invoked to make it more user-friendly. The testing will be done in one or two weeks, I hope.

Cheers,
Guanliang Meng

from mitoz.

Dear Guanliang,
Thanks for your kind answer. The MitoZ is actually very well written and I don't have any issue running it locally. ete3 FTP issue is an issue that we need to address to ete3 team.
Looking forward to test version2.
Cheers
Arsalan

from mitoz.

Dear Arsalan,

Thank you very much!

Now I'm going to close the issue. Please open new issues if you have questions.

from mitoz.

Closed since the limitation is from ETE3 package.

from mitoz.