Admin: Dan Tenenbaum
Dan Tenenbaum ♦♦ 8.1k
- Reputation:
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- Joined:
- 6 years, 10 months ago
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- d*******@fhcrc.org
I was in the Bioconductor group at Fred Hutchinson Cancer Research Center in Seattle, WA, USA.
Posts by Dan Tenenbaum
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... Since the last time I contributed to this thread, I've become aware of AWS Batch. You might want to look at that.
Whatever you do, I'd focus on keeping things simple. If you try to get CfnCluster to work, I'd start by just trying to get a simple cluster to work (with a basic AMI like one of the Ale ...
written 4 months ago by
Dan Tenenbaum ♦♦ 8.1k
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... StarCluster is a little old. Look info CfnCluster: https://github.com/awslabs/cfncluster .
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written 5 months ago by
Dan Tenenbaum ♦♦ 8.1k
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... That would be a bit tricky as we are trying to base our images on rocker's, so it seems best (from our point of view) to start by depending on their rstudio images, and not add rstudio ourselves at the end. Otherwise we don't get the benefit of the work they have already done.
Your Dockerfile can b ...
written 13 months ago by
Dan Tenenbaum ♦♦ 8.1k
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... The docker containers could be based on r-base, but then people might complain that they don't have RStudio.
So I guess it's a question of what is more valuable to more people, being able to use RStudio out of the box with Biooconductor Docker containers, or not having RStudio in order to comply w ...
written 13 months ago by
Dan Tenenbaum ♦♦ 8.1k
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... R is not giving you a chance to say whether you want to install packages from source, and then it fails when it can't find the tools (such as 'make') needed to install packages from source.
So you have two choices:
1) Tell R to a) either ask you before installing packages from source, or b) to nev ...
written 13 months ago by
Dan Tenenbaum ♦♦ 8.1k
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Comment:
C: edgeR installation issue
... OK, R is not giving you a chance to say "go ahead and install the binary version even though there is a newer source version". You can change this behavior by doing
options(install.packages.compile.from.source="interactive")
Before you run biocLite().
Then when it asks you whether to install the ...
written 13 months ago by
Dan Tenenbaum ♦♦ 8.1k
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Comment:
C: edgeR installation issue
... The easiest way is to install the Mac binary (i.e., don't build from source):
source('https://bioconductor.org/biocLite.R')
biocLite("edgeR", type="binary")
If you need/want to build from source, download and install gfortran-4.2.3.pkg from
https://cran.r-project.org/bin/macosx/tools/
If you sti ...
written 13 months ago by
Dan Tenenbaum ♦♦ 8.1k
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Comment:
C: Error in loading rsbml
... Yeah, something sounds wrong. According to http://sbml.org/Software/libSBML, the latest stable version is 5.13.0. Please thoroughly remove libsbml and then install version 5.10 from here.
...
written 13 months ago by
Dan Tenenbaum ♦♦ 8.1k
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Comment:
C: Can't load package "org.Hs.eg.db"
... So do you mean the problem is solved? If so I will mark this thread as answered.
...
written 13 months ago by
Dan Tenenbaum ♦♦ 8.1k
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274
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Comment:
C: Error in loading rsbml
... The build macs use version 5.10.x
...
written 13 months ago by
Dan Tenenbaum ♦♦ 8.1k
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