Question: BiomaRt and phytozome
0
gravatar for s.nielsen
10 days ago by
s.nielsen0
s.nielsen0 wrote:

Any idea how to connect to phytozome through biomart? It seems to be an Rcurl problem when digging into the biomaRt code. Specifically, getURL. Something to do with SSL certificates?

library(biomaRt) library(RCurl) phyto <- "https://phytozome.jgi.doe.gov" listMarts(host = phyto)

Request to BioMart web service failed. The BioMart web service you're accessing may be down. Check the following URL and see if this website is available: https://phytozome.jgi.doe.gov:80/biomart/martservice?type=registry&requestid=biomaRt Error in if (!grepl(x = registry, pattern = "^\n*<martregistry>")) { : argument is of length zero

getURL(phyto)

Error in function (type, msg, asError = TRUE) : error:1407742E:SSL routines:SSL23GETSERVER_HELLO:tlsv1 alert protocol version

url.exists(phyto)

[1] FALSE >

sessionInfo()

R version 3.5.1 (2018-07-02) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale: [1] LCCOLLATE=EnglishUnited Kingdom.1252 LCCTYPE=EnglishUnited Kingdom.1252 LCMONETARY=EnglishUnited Kingdom.1252 [4] LCNUMERIC=C LCTIME=English_United Kingdom.1252

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] RCurl1.95-4.12 bitops1.0-6 biomaRt_2.38.0

biomart rcurl phytozome • 39 views
ADD COMMENTlink modified 10 days ago by Mike Smith3.6k • written 10 days ago by s.nielsen0
Answer: BiomaRt and phytozome
0
gravatar for Mike Smith
10 days ago by
Mike Smith3.6k
EMBL Heidelberg / de.NBI
Mike Smith3.6k wrote:

Try setting the port to 443 since you're using https e.g.

listMarts(host = phyto, port = 443)
                    biomart                  version
1            phytozome_mart V12 Genomes and Families
2 phytozome_diversity__mart     V12 Genome Diversity
3    phytozome_mart_archive           Genome Archive

I thought I'd modified biomaRt to try and do this automatically, but maybe it was only for Ensembl. I'll add a patch to use the appropriate port for the protocol unless overridden by the user.

ADD COMMENTlink modified 10 days ago • written 10 days ago by Mike Smith3.6k

I think there may be a network issue at play here? I still have the error. I'm currently at my university. I may try at home and see what happens.

ADD REPLYlink written 9 days ago by s.nielsen0

What happens if you follow the instruction in the error message and go to https://phytozome.jgi.doe.gov:80/biomart/martservice?type=registry&requestid=biomaRt in a browser?

I expect that should fail with a protocol error, so maybe it's more informative to visit https://phytozome.jgi.doe.gov:443/biomart/martservice?type=registry&requestid=biomaRt

ADD REPLYlink written 9 days ago by Mike Smith3.6k

So with port 433, the web link works..

But through R it does not;

library(RCurl)

getURL('https://phytozome.jgi.doe.gov:443/biomart/martservice?type=registry&requestid=biomaRt')

Error in function (type, msg, asError = TRUE) : error:1407742E:SSL routines:SSL23GETSERVER_HELLO:tlsv1 alert protocol version

I've asked some friends off campus to try, and it works for them so it must be something with my university internet (proxy settings or something. I'm about to ask IT).

ADD REPLYlink written 9 days ago by s.nielsen0
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