Steps to download all the databases and setup manually in DRAM

[srisvs33]

Dear developers @jrr-microbio @rmFlynn @shafferm

For some reason, the database download got interrupted / or not successful in our HPC clusters. So, I am thinking about downloading all the latest databases manually and setup in our clusters. Could you please assist with the steps to follow to do the same along with links to all the databases. I remember somewhere in the post previously. however, now I am unable to find that post.

Thank you very much

Venkat

[smdabdoub]

Here is the list of databases:

• kofam_hmm
• kofam_ko_list
• uniref
• pfam
• pfam_hmm
• dbcan
• dbcan_fam_activities
• dbcan_subfam_ec
• vogdb
• vog_annotations
• viral
• peptidase
• genome_summary_form
• module_step_form
• function_heatmap_form
• amg_database
• etc_module_database

They can be individually updated through:

DRAM-setup.py prepare databases --select_db <database>.

Note that the --select_db parameter can be used multiple times in a single command:

DRAM-setup.py prepare_databases --select_db pfam --select_db pfam_hmm --output_dir database_dir

[fischuu]

I think that solution has the problem, that the DRAM-setup.py ... call throws then an error telling that the output_dir folder exists already (at least for me this happens).