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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 8 months ago

claramicro commented 8 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 8 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 8 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