Hi! I've reproduced the targeted analysis in the TOSCA paper, using data provided by PRJEB36436.
Issue
In rules/database.smk rule download_database fails because the URL for ESP6500SI returns 404. The error is not reported until a later job tries to unzip the (broken) archive complaining about tar being unable to detect archive data.
Possible solution
As a drop in solution I've changed the hardcoded URL in config/<yourconfig>.yaml from:
This holds for both GRCh38 and GRCh37 and works. The only copy available for download of that file I've found is a snapshot from the internet archive. I'm not sure about them being happy about people directly linking or downloading from them (they suggest using their own cli client).
Hi! I've reproduced the targeted analysis in the TOSCA paper, using data provided by PRJEB36436.
Issue In
rules/database.smkruledownload_databasefails because the URL for ESP6500SI returns 404. The error is not reported until a later job tries to unzip the (broken) archive complaining about tar being unable to detect archive data.Possible solution As a drop in solution I've changed the hardcoded URL in
config/<yourconfig>.yamlfrom:to:
This holds for both GRCh38 and GRCh37 and works. The only copy available for download of that file I've found is a snapshot from the internet archive. I'm not sure about them being happy about people directly linking or downloading from them (they suggest using their own cli client).