Getting problem when I type "./download_dbs.sh"

ThomasYang0615 commented 4 months ago

Hello, I have problem at the final step of installing megSAP : ./download_dbs.sh

When I execute '''download_dbs.sh''' :

I can't Install CancerHotspots.org, the address of row 25 seems broken
- wget https://www.cancerhotspots.org/files/hotspots_v2.xls
I can't Install ClinVar, there will be ERROR:
- Error in get_ref_seq : Failed to open the file /tmp/local_ngs_data//GRCh38.fa
- [faidx] Could not build fai index /tmp/local_ngs_data//GRCh38.fa.fai

I did try to find out the solution, but I stuck. Can you give me a hand?

noob9721 commented 3 weeks ago

Hello, Did you get a solution for this by any chance? I have the same problem.

marc-sturm commented 3 weeks ago

Which version of megSAP are u using? 2023_11 or the master?

CancerHotspots: the URL should work when using the master

Clinvar: please use the latest master, I just comitted a fix, see 3e253ccda9f9a4fb5a5fd004fc4337d5a09975da

Does it work with the master?

imgag / megSAP