setup_db.pl failing to download SSU data

[hans-vg]

Here is the code I am running and the errors below.

docker run --shm-size 2g --rm -u $(id -u):$(id -g) -it -v /Users/hvasquezgross/test_docker/:/data/ xiaolidong/docker-metaerg setup_db.pl -o /data
[Wed Mar 10 20:42:05 2021] construct db directories
[Wed Mar 10 20:42:05 2021] Fetching SILVA_132_SSURef_Nr99_tax_silva_trunc.fasta.gz
Fetch failed! HTTP response: 404 Not Found [404 Not Found] at /NGStools/metaerg/bin/setup_db.pl line 761.
Command failed:  at /NGStools/metaerg/bin/setup_db.pl line 761.
Command failed:  at /NGStools/metaerg/bin/setup_db.pl line 761.

Since we received a 404 HTTP error, I did some digging and found the cause of the error. The perl script is trying to download a link: "https://www.arb-silva.de/fileadmin/silva_databases/release_$ssu_version/Exports/$file.gz"

It looks like $ssu_version is hardcoded as 138 at the top of the perl script. The $file is hardcoded as "SILVA_138.1_SSURef_NR99_tax_silva_trunc.fasta". So the formatted HTTP link its trying to download is: "https://www.arb-silva.de/fileadmin/silva_databases/release_138/Exports/SILVA_138.1_SSURef_NR99_tax_silva_trunc.fasta.gz" which does return a 404 error.

However, the correct $ssu_version should be 138_1 and correct link should be: https://www.arb-silva.de/fileadmin/silva_databases/release_138_1/Exports/SILVA_138.1_SSURef_NR99_tax_silva_trunc.fasta.gz

It may be nice to have a -vssu and -vlsu version option to configure the correct URL to download these files. Right now, we have no way of setting up the database to run Metaerg within the docker image unless the setup_db.pl is updated.