ftp for clinvar true set has changed

[edgarjavi]

There is a new version of the vcf in clinvar, the file with the 20170802 data is archived. Here is the new line of code from the make.sh file with the new location

wget ftp://ftp.ncbi.nih.gov/pub/clinvar/vcf_GRCh37/vcf2.0/archive/2017/clinvar${date}.vcf.gz

[jimhavrilla]

That's already in the make.sh

Jim Havrilla PhD Candidate in Human Genetics, University of Utah Accelerated BS/MS in Biomedical Engineering, Drexel University '12, Concentration: Bioinformatics "Memory, comprehension, communication, motivation"

On Mon, Sep 11, 2017 at 3:13 PM, Javier notifications@github.com wrote:

There is a new version of the vcf in clinvar, the file with the 20170802 data is archived. Here is the new line of code from the make.sh file with the new location

wget ftp://ftp.ncbi.nih.gov/pub/clinvar/vcf_GRCh37/vcf2.0/ archive/2017/clinvar${date}.vcf.gz

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[jimhavrilla]

You mean the september one is new? ftp://ftp.ncbi.nih.gov/pub/clinvar/vcf_GRCh37/vcf_2.0/clinvar_20170905.vcf.gz ?

Jim Havrilla PhD Candidate in Human Genetics, University of Utah Accelerated BS/MS in Biomedical Engineering, Drexel University '12, Concentration: Bioinformatics "Memory, comprehension, communication, motivation"

On Mon, Sep 11, 2017 at 3:15 PM, Jim Havrilla semjaavria@gmail.com wrote:

That's already in the make.sh

Jim Havrilla PhD Candidate in Human Genetics, University of Utah Accelerated BS/MS in Biomedical Engineering, Drexel University '12, Concentration: Bioinformatics "Memory, comprehension, communication, motivation"

On Mon, Sep 11, 2017 at 3:13 PM, Javier notifications@github.com wrote:

There is a new version of the vcf in clinvar, the file with the 20170802 data is archived. Here is the new line of code from the make.sh file with the new location

wget ftp://ftp.ncbi.nih.gov/pub/clinvar/vcf_GRCh37/vcf2.0/archiv e/2017/clinvar${date}.vcf.gz

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[edgarjavi]

yeah the clinvar make.sh wont run because the ftp location is outdated

[jimhavrilla]

I will update the date then.

Jim Havrilla PhD Candidate in Human Genetics, University of Utah Accelerated BS/MS in Biomedical Engineering, Drexel University '12, Concentration: Bioinformatics "Memory, comprehension, communication, motivation"

On Mon, Sep 11, 2017 at 3:20 PM, Javier notifications@github.com wrote:

yeah the clinvar make.sh wont run because the ftp location is outdated

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[jimhavrilla]

Or do you recommend we move to the archive location?

Jim Havrilla PhD Candidate in Human Genetics, University of Utah Accelerated BS/MS in Biomedical Engineering, Drexel University '12, Concentration: Bioinformatics "Memory, comprehension, communication, motivation"

On Mon, Sep 11, 2017 at 3:21 PM, Jim Havrilla semjaavria@gmail.com wrote:

I will update the date then.

Jim Havrilla PhD Candidate in Human Genetics, University of Utah Accelerated BS/MS in Biomedical Engineering, Drexel University '12, Concentration: Bioinformatics "Memory, comprehension, communication, motivation"

On Mon, Sep 11, 2017 at 3:20 PM, Javier notifications@github.com wrote:

yeah the clinvar make.sh wont run because the ftp location is outdated

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[edgarjavi]

Exactly, the line I sent above gets the file with the old date.

[jimhavrilla]

Actually I think I have a fix. I can try to pull if the newest one is there and exists, otherwise, check the archive for the date. This will probably need to be changed in 2018 as well, since the archives will shift there. Probably a constantly mutable make.sh to stay up-to-date. Thanks for making me aware of it. I'll push a fix.

[brentp]

let's keep it so it points to the latest file in the archive directory.

[jimhavrilla]

done.