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Clinical-Genomics / fusion-report

Tool for parsing outputs from fusion detection tools. Part of a nf-core/rnafusion pipeline. Checkout a live demo at https://matq007.github.io/fusion-report/example/

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Cannot download more than 78% / 100MB of TCGA_ChiTaRS_combined_fusion_ORF_analyzed_gencode_h19v19.txt

valleema opened this issue · comments

commented

Hello,

I tried to automatically download references through nf-core/rnafusion, the download get stuck at 78% or around 100MB.

Then, I tried manually to download, as proposed here : https://matq007.github.io/fusion-report/#/download?id=manual-download

The line:

wget --no-check-certificate https://ccsm.uth.edu/FusionGDB/tables/TCGA_ChiTaRS_combined_fusion_ORF_analyzed_gencode_h19v19.txt -O TCGA_ChiTaRS_combined_fusion_ORF_analyzed_gencode_h19v19.txt

Gets stuck at 78% or ~ 100MB (tried on different machines, local and distant to me).

Running with -c helps completing the download, after killing by CTRL-C the previous wget process:

wget -c --no-check-certificate https://ccsm.uth.edu/FusionGDB/tables/TCGA_ChiTaRS_combined_fusion_ORF_analyzed_gencode_h19v19.txt -O TCGA_ChiTaRS_combined_fusion_ORF_analyzed_gencode_h19v19.txt

But even if I have found a workaround, I am stuck, because in the help, you say;

# Create database and import the data

...but I don't know how do you do it.

commented

I am sorry, but it has just worked as intended, without getting stuck... I have no idea why!!