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Can't download resource data of oncotator

Hi all,
I failed to download resource data provided by README and cann't on the Internet. Could someone post the correct links here. Thanks very much.
Here are the three failed links.
https://tcga-data.nci.nih.gov/docs/GAF/GAF3.0/transcript.genome.v3_0.gaf.gz
https://tcga-data.nci.nih.gov/docs/GAF/GAF3.0/UCSCgene.Jan2012.v3_0.fa.gz
wget ftp://ftp.sanger.ac.uk/pub/CGP/cosmic/data_export/CosmicMutantExportIncFus_v62_291112.tsv.gz

Answers

  • shleeshlee CambridgeMember, Broadie, Moderator

    Hi @liangadam,

    It appears that the TCGA Data Portal stopped running July 15, 2016. Here's the message I see on their site:

    The TCGA Data Portal is no longer operational and all TCGA data now resides at the Genomic Data Commons. We have provided a link to the following resource which should help in continuing to access and interpret TCGA data.

    And the GDC (NCI Genomic Data Commons), where specific data has migrated to, is currently "undergoing unscheduled maintenance".

    Can you check the GDC site for your data files when they're back up again? In the meanwhile, I'll also ask around to see what is going on and have the README corrected. Thanks for letting us know.

  • LeeTL1220LeeTL1220 Arlington, MAMember, Broadie, Dev

    @liangadam That README is out of date (by years) and will be deleted. It is an accident that it still exists.

  • shleeshlee CambridgeMember, Broadie, Moderator

    Thanks @LeeTL1220 for letting us know.

    @liangadam, you can find general installation and running instruction in our GATK forum post here and at the github site here. Let us know if you have issues running the tool.

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