Skip to content

Update database_installation.md #462

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
PierreFoucault wants to merge 1 commit into
base: master
Choose a base branch
from
Open

Update database_installation.md #462

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
9 changes: 9 additions & 0 deletions installation/database_installation.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -35,6 +35,15 @@ Note: Compared to Kraken1, the Kraken2 database is considerably more compact, ma
``` bash
kraken2-build --standard --threads 24 --db MY_KRAKEN2_DB
```
Due to changes in the link to NCBI's databases, you may need to change 2 line of the KRAKEN2 scripts, as proposed in the KRAKEN2 issue section.

Search for the file: download_genomic_library.sh,line 17 change FTP_SERVER="**ftp**://$NCBI_SERVER" to FTP_SERVER="**https**://$NCBI_SERVER"
then search for the file: rsync_from_ncbi.pl, line 46 change if (! ($full_path =~ s#^ftp://${qm_server}${qm_server_path}/##)) { to if (! ($full_path =~ s#^https://${qm_server}${qm_server_path}/##)) {

source: https://github.com/DerrickWood/kraken2/commit/493568d3f44753f8f711634f86fbaab1b9dfb071
https://github.com/DerrickWood/kraken2/commit/4f648f5a83498f666193be7b9b71a38e3b99ee24
https://github.com/DerrickWood/kraken2/issues/518

Do not forget to set the KRAKEN_DB variable in the config-metawrap file! Run `which config-metawrap` to find it.
``` bash
KRAKEN2_DB=/path/to/my/database/MY_KRAKEN2_DATABASE
Expand Down