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nmquijada / tormes

Making whole bacterial genome sequencing data analysis easy
GNU General Public License v3.0
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installing kraken2 database #72

Open claramicro opened 10 months ago

claramicro commented 10 months ago

while tormes-setup there is no conection with the web Connecting nto ftp.ccb.jhu.edu (ftp.ccb.jhu.edu) \128.220.174.63\ :21...failed: Conection timed out

I think that since 2020 the downloading of kraken2 database have changed but i dont know how to avoid the step in the instalation. Thks you so much

Clara

biobrad commented 10 months ago

Hi Clara, sorry for the late response. You are right, that link appears to no longer work. I am working on a fix and will advise when completed.

biobrad commented 10 months ago

Hi Clara, This fix should work.

you need to run the following commands on the 'tormes-setup' file that will be located in your (conda or mambaforge)/envs/tormes-1.3.0/bin folder.

The commands can be run 'as is' one at a time. the '*' in the filepath allows the command to work with either conda or mamba installation directories. 

rm -ri ~/*/envs/tormes-1.3.0/db/minikraken-DB

sed -i 's@ftp:\/\/ftp\.ccb\.jhu\.edu\/pub\/data\/kraken2_dbs\/minikraken_8GB_202003\.tgz@https:\/\/genome-idx.s3.amazonaws.com\/kraken\/k2_standard_08gb_20231009.tar.gz@g' ~/*/envs/tormes-1.3.0/bin/tormes-setup

sed -i 's/minikraken_8GB_202003.tgz/k2_standard_08gb_20231009.tar.gz/g' ~/*/envs/tormes-1.3.0/bin/tormes-setup

sed -i 's@\/minikraken_8GB_20200312@@g' ~/*/envs/tormes-1.3.0/bin/tormes-setup

after you have run these commands, activate your tormes environment and run the tormes-setup step of the installation again.

let me know how you go.

cheers Brad