transvar configuration and datafiles
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5.6 years ago
nkinney06 ▴ 90

I am trying to install the reverse annotation program transvar: http://transvar.readthedocs.io/en/latest/download_and_install.html

once you install with pip you have to configure by downloading the annotation files:

transvar config --download_anno --refversion hg19

when I run this command I get the following output:

[bakdownloading] /home/nick/.transvar.download/hg19.refseq.gff.gz.transvardb ...Done (0.0 MB). [bakdownloading] /home/nick/.transvar.download/hg19.refseq.gff.gz.transvardb.gene_idx ...Done (0.0 MB). [bakdownloading] /home/nick/.transvar.download/hg19.refseq.gff.gz.transvardb.trxn_idx ...Done (0.0 MB). ...

now I do get files in the transvar download directory, but they appear to contain error messages; for example,

> ... <h1>Web Page Blocked</h1> <p>Access to the web page you were trying
> to visit has been blocked in accordance with company policy. Please
> contact your system administrator if you believe this is in error.</p>
> <p> ...

I dont thik this error is coming from my end. Im wondering if anyone has succeeded in installing transvar? I have also tried installing from source but cant even get this far. Possibly all I need are the annotation files and I could configure transvar by telling the program where they are. I am listing all the annotation files here in case anyone knows where I might be able to find them; thanks for the help.

hg19.aceview.gff.gz.transvardb hg19.aceview.gff.gz.transvardb.gene_idx hg19.aceview.gff.gz.transvardb.loc_idx hg19.aceview.gff.gz.transvardb.loc_idx.tbi hg19.aceview.gff.gz.transvardb.trxn_idx hg19.ccds.txt.transvardb hg19.ccds.txt.transvardb.gene_idx hg19.ccds.txt.transvardb.loc_idx hg19.ccds.txt.transvardb.loc_idx.tbi hg19.ccds.txt.transvardb.trxn_idx hg19.ensembl.gtf.gz.transvardb hg19.ensembl.gtf.gz.transvardb.gene_idx hg19.ensembl.gtf.gz.transvardb.loc_idx hg19.ensembl.gtf.gz.transvardb.loc_idx.tbi hg19.ensembl.gtf.gz.transvardb.trxn_idx hg19.fa hg19.fa.fai hg19.gencode.gtf.gz.transvardb hg19.gencode.gtf.gz.transvardb.gene_idx hg19.gencode.gtf.gz.transvardb.loc_idx hg19.gencode.gtf.gz.transvardb.loc_idx.tbi hg19.gencode.gtf.gz.transvardb.trxn_idx hg19.knowngene.gz.transvardb hg19.knowngene.gz.transvardb.gene_idx hg19.knowngene.gz.transvardb.loc_idx hg19.knowngene.gz.transvardb.loc_idx.tbi hg19.knowngene.gz.transvardb.trxn_idx hg19.refseq.gff.gz.transvardb hg19.refseq.gff.gz.transvardb.gene_idx hg19.refseq.gff.gz.transvardb.loc_idx hg19.refseq.gff.gz.transvardb.loc_idx.tbi hg19.refseq.gff.gz.transvardb.trxn_idx hg19.ucsc.txt.gz.transvardb hg19.ucsc.txt.gz.transvardb.gene_idx hg19.ucsc.txt.gz.transvardb.loc_idx hg19.ucsc.txt.gz.transvardb.loc_idx.tbi hg19.ucsc.txt.gz.transvardb.trxn_idx

software error • 2.0k views
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