where is the database

[chaoyanggu]

I downloaded the install package ，and I want to use the test data that comes with the software for testing; but I don’t know what the path of the database refers to, I can not found a detailed description. How can I running the shell in tests?

test data:/software/fusion-report-master/tests/test_data/
data:/software/fusion-report-master/fusion_report/data/schema/ ?

thanks

[chaoyanggu]

fusion_report download
--cosmic_usr ''
--cosmic_passwd ''
/path/to/db
whether the above codes can download the data of three databases (FusionGDB, Mitelman, COSMIC), or it only can download the data from COSMIC;

I download the data from the website https://ccsm.uth.edu/FusionGDB/index.html; and
sqlite3 fusiongdb.db < /software/fusion-report-master/fusion_report/data/schema//FusionGDB.sql

but it does not work; error :sqlite3.OperationalError: no such table: tcga_chitars_combined_fusion_information_on_hg19

[Martin Proks]

Hi @chaoyanggu, the fusion_report download will download all datasets. You have to provide the credentials for COSMIC, as this is the only database that requires authentication. The process will download the databases to your specified path, you have to replace /path/to/db to your system for example ~/Desktop.

Regarding the test data, you will have to download them from repo and then just specify the path the directory.

[chaoyanggu]

I registered a COSMIC account for login , the user name is my email, and then I used the email and password to download the database,
the codes is:
/software/fusion-report-master/bin/fusion_report download --cosmic_usr '[e-mail]' --cosmic_passwd '' ./db/,

but the following error occurred;
fusion_report.common.exceptions.app.AppException: HTTP Error 302: The HTTP server returned a redirect error that would lead to an infinite loop.
The last 30x error message was:
Found
HTTP Error 302: The HTTP server returned a redirect error that would lead to an infinite loop.
The last 30x error message was:
Found

is there any other way to download the data？
thanks

[Martin Proks]

Hi, this seems like some kind of a network issue. Are you behind a proxy?
I've installed the tool over with conda and ran the download myself without any issue. Could try running it on your machine instead of server?
Note to myself: possible cookie issue ? ref

[Martin Proks]

After experiencing this issue in nf-core/rnafusion, this is a firewall issue. The access to ftp is blocked, so if you have still issues with downloading you will have to install the package on your work notebook and then transfer the database to cluster.