[Bioc-devel] Issue with GenomeInfoDb

[Martin Morgan]

Thanks Ken the list filters attachements that are not of the following type

text/x-diff
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so please feel free to send again (or to me and I'll see that it gets 
posted.

Martin


On 07/17/2017 02:37 PM, Weiss, Kenneth wrote:
> Greetings,
> 
> Attached is the patch file GenomeInfoDb.patch noted below.
> 
> Cheers,
> Ken
> 
> From: Weiss, Kenneth
> Sent: Monday, July 17, 2017 11:33 AM
> To: 'bioc-devel at r-project.org'
> Cc: Mark Montague (markmont at umich.edu)
> Subject: Issue with GenomeInfoDb
> 
> Greetings,
> 
> I provide support for an HPC cluster at the University of Michigan. Recently we had a user approach us with the following problem:
> 
> I have an issue about using the following package/function in R.
> 
> *library("GenomeInfoDb")*
> *GenomeInfoDb::Seqinfo(genome = "mm10")*
> 
> The function is getting a remote resource that works on the head node, but
> not the worker nodes. The error on worker nodes is as follows.
> *Error in .make_assembly_report_URL(assembly_accession)*
> 
> We have our cluster setup to use proxy variables to be able to access the internet from our compute nodes. After some digging, my colleague, Mark Montague, was able to come up with the following work around:
> 
> This is not a security issue. The problem is that our cluster compute nodes are not connected to the Internet.
> Because of this, compute nodes need to use a proxy server in order to access things that are off campus. Usually this
> is not a problem, but in this particular case there are actually three problems related to GenomeInfoDb not working
> correctly with the proxy when running on compute nodes:
> 
> 1. GenomeInfoDb doesn't recognize the FTP directory listing format our proxy server uses.
> 2. GenomeInfoDb is not handing the download of assembly reports in the same way it handles other downloads, which is a
> problem when the proxy is being used.
> 3. R is not always using the proxy for FTP connections; this appears to be a quirk of R.
> 
> To fix problems 1 and 2, you can install a modified version of GenomeInfoDb to replace the one you currently have
> installed in your home directory by running the following commands:
> 
> cd ~
> git clone https://github.com/Bioconductor-mirror/GenomeInfoDb.git
> cd GenomeInfoDb
> git checkout release-3.4
> patch -p 1 < /home/someuser/GenomeInfoDb.patch
> R CMD INSTALL .
> 
> To fix problem 3, you need to tell R to use libcurl to download files rather than its default method. This needs to be
> done in every R script that uses GenomeInfoDb. For example:
> 
> options(download.file.method="libcurl")
> library("GenomeInfoDb")
> GenomeInfoDb::Seqinfo(genome = "mm10")
> 
> Alternatively, you can put the "options" command above into a file named /home/someuser/.Rprofile and it will take effect
> for all R scripts you run.
> 
> Just thought you would like to know.
> 
> Cheers,
> Ken
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