Hey Bjoern,

I'm trying to use variant_recalibrator, xy_plot and other tools that depend on package_r_2_11_0 and require ggplot2 to be installed. Since CRAN support for R 2.11.0 and 2.15.0 is on the out, perhaps its a better idea to update the packages the depend on those versions to R 3.0 or 3.1? The variant_recalibrator tool generates an Rscript incompatible with modern versions of ggplot2, so this could be a quite involved undertaking.

Meanwhile I'll look into the download_store option. You download all of the tarballs and install them individually with R CMD INSTALL?

Cheers,

-E -Evan Bollig Research Associate | Application Developer | User Support Consultant Minnesota Supercomputing Institute 599 Walter Library 612 624 1447 evan@msi.umn.edu boll0107@umn.edu

On Tue, Jul 29, 2014 at 2:46 PM, Björn Grüning bjoern.gruening@gmail.com wrote:

Hi Evan,

do you have somehow access to this tarball? Than we can put it on

https://github.com/bgruening/download_store

I use that to host R packages to save them for reproducibility.

...

Can I install another package_r and have packages that depend on package_r_2_11_0 use the newer version?

I don't think so. But that depends very much on your package. Is it not possible to use a newer R version? In either case you should save all tarballs somehow to archive them!

Cheers, Bjoern

...

-Evan Bollig Research Associate | Application Developer | User Support Consultant Minnesota Supercomputing Institute 599 Walter Library 612 624 1447 evan@msi.umn.edu boll0107@umn.edu ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/

Bjoern,

FYI, I found that package_gatk_1_4 from the main Galaxy toolshed produces Rscript files for VariantRecalibrator and other commands that require ggplot_0.8.8 and reshape_0.8.4. This applies to GATK versions 1.4-20 and 1.4-37.

The magic incantation to get a systemwide R v3.1 setup properly is:

r <- getOption("repos"); r["CRAN"] <- "http://cran.rstudio.com/"; options(repos=r); install.packages(c('devtools','gsalib')); require(devtools); install_url('http://cran.r-project.org/src/contrib/Archive/plyr/plyr_1.7.1.tar.gz'); install_url('http://cran.r-project.org/src/contrib/Archive/reshape/reshape_0.8.4.tar.gz'); install_url('http://cran.r-project.org/src/contrib/Archive/ggplot2/ggplot2_0.8.8.tar.gz');

I'm not sure gsalib is required, but it is better to play it safe IMO.

Can you add this to the package_gatk_1_4 documentation to help others along? It would be even better if the package_gatk_1_4 could also install those R libraries itself.

Cheers,

-E -Evan Bollig Research Associate | Application Developer | User Support Consultant Minnesota Supercomputing Institute 599 Walter Library 612 624 1447 evan@msi.umn.edu boll0107@umn.edu

On Tue, Jul 29, 2014 at 4:22 PM, Björn Grüning bjoern.gruening@gmail.com wrote:

Am 29.07.2014 um 22:45 schrieb Evan Bollig:

...

Hey Bjoern,

I'm trying to use variant_recalibrator, xy_plot and other tools that depend on package_r_2_11_0 and require ggplot2 to be installed. Since CRAN support for R 2.11.0 and 2.15.0 is on the out, perhaps its a better idea to update the packages the depend on those versions to R 3.0 or 3.1?

Yes, this would be a better idea!

...

The variant_recalibrator tool generates an Rscript incompatible with modern versions of ggplot2, so this could be a quite involved undertaking.

Oh :( ... can we somehow get an old tarball of ggplot2? Have you looked at older linux disributions, debian stable for example?

I found ggplot on download_store ;) https://github.com/bgruening/download_store/blob/master/gatk2_R_deps/ggplot2...

Is that old enough?

...

Meanwhile I'll look into the download_store option. You download all of the tarballs and install them individually with R CMD INSTALL?

Not really, we have a nice routine in the toolshed for such tasks: Have a look at: https://github.com/bgruening/galaxytools/tree/master/orphan_tool_dependencie...

Note: the order of the packages are important ...

Ciao, Bjoern

...

Cheers,

-E -Evan Bollig Research Associate | Application Developer | User Support Consultant Minnesota Supercomputing Institute 599 Walter Library 612 624 1447 evan@msi.umn.edu boll0107@umn.edu

On Tue, Jul 29, 2014 at 2:46 PM, Björn Grüning bjoern.gruening@gmail.com wrote:

...

Hi Evan,

do you have somehow access to this tarball? Than we can put it on

https://github.com/bgruening/download_store

I use that to host R packages to save them for reproducibility.

...

Can I install another package_r and have packages that depend on package_r_2_11_0 use the newer version?

I don't think so. But that depends very much on your package. Is it not possible to use a newer R version? In either case you should save all tarballs somehow to archive them!

Cheers, Bjoern

...

-Evan Bollig Research Associate | Application Developer | User Support Consultant Minnesota Supercomputing Institute 599 Walter Library 612 624 1447 evan@msi.umn.edu boll0107@umn.edu ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/

Btw, I forgot: plyr_1.7.1 is also required for package_gatk_1_4. Hence the install_url call for it below.

-E -Evan Bollig Research Associate | Application Developer | User Support Consultant Minnesota Supercomputing Institute 599 Walter Library 612 624 1447 evan@msi.umn.edu boll0107@umn.edu

On Thu, Jul 31, 2014 at 1:51 PM, Björn Grüning bjoern.gruening@gmail.com wrote:

Hi Evan,

unfortunately I have no access to this repository. I'm only the maintainer of the galaxytools in github. But I have CC'ed Dave, he is responsible for the devteam packages!

Cheers and thanks for sharing your information! Bjoern

Am 31.07.2014 um 20:47 schrieb Evan Bollig:

...

Bjoern,

FYI, I found that package_gatk_1_4 from the main Galaxy toolshed produces Rscript files for VariantRecalibrator and other commands that require ggplot_0.8.8 and reshape_0.8.4. This applies to GATK versions 1.4-20 and 1.4-37.

The magic incantation to get a systemwide R v3.1 setup properly is:

r <- getOption("repos"); r["CRAN"] <- "http://cran.rstudio.com/"; options(repos=r); install.packages(c('devtools','gsalib')); require(devtools);

install_url('http://cran.r-project.org/src/contrib/Archive/plyr/plyr_1.7.1.tar.gz');

install_url('http://cran.r-project.org/src/contrib/Archive/reshape/reshape_0.8.4.tar.gz');

install_url('http://cran.r-project.org/src/contrib/Archive/ggplot2/ggplot2_0.8.8.tar.gz');

I'm not sure gsalib is required, but it is better to play it safe IMO.

Can you add this to the package_gatk_1_4 documentation to help others along? It would be even better if the package_gatk_1_4 could also install those R libraries itself.

Cheers,

-E -Evan Bollig Research Associate | Application Developer | User Support Consultant Minnesota Supercomputing Institute 599 Walter Library 612 624 1447 evan@msi.umn.edu boll0107@umn.edu

On Tue, Jul 29, 2014 at 4:22 PM, Björn Grüning bjoern.gruening@gmail.com wrote:

...

Am 29.07.2014 um 22:45 schrieb Evan Bollig:

...

Hey Bjoern,

I'm trying to use variant_recalibrator, xy_plot and other tools that depend on package_r_2_11_0 and require ggplot2 to be installed. Since CRAN support for R 2.11.0 and 2.15.0 is on the out, perhaps its a better idea to update the packages the depend on those versions to R 3.0 or 3.1?

Yes, this would be a better idea!

...

The variant_recalibrator tool generates an Rscript incompatible with modern versions of ggplot2, so this could be a quite involved undertaking.

Oh :( ... can we somehow get an old tarball of ggplot2? Have you looked at older linux disributions, debian stable for example?

I found ggplot on download_store ;)

https://github.com/bgruening/download_store/blob/master/gatk2_R_deps/ggplot2...

Is that old enough?

...

Meanwhile I'll look into the download_store option. You download all of the tarballs and install them individually with R CMD INSTALL?

Not really, we have a nice routine in the toolshed for such tasks: Have a look at:

https://github.com/bgruening/galaxytools/tree/master/orphan_tool_dependencie...

Note: the order of the packages are important ...

Ciao, Bjoern

...

Cheers,

-E -Evan Bollig Research Associate | Application Developer | User Support Consultant Minnesota Supercomputing Institute 599 Walter Library 612 624 1447 evan@msi.umn.edu boll0107@umn.edu

On Tue, Jul 29, 2014 at 2:46 PM, Björn Grüning bjoern.gruening@gmail.com wrote:

...

Hi Evan,

do you have somehow access to this tarball? Than we can put it on

https://github.com/bgruening/download_store

I use that to host R packages to save them for reproducibility.

...

Can I install another package_r and have packages that depend on package_r_2_11_0 use the newer version?

I don't think so. But that depends very much on your package. Is it not possible to use a newer R version? In either case you should save all tarballs somehow to archive them!

Cheers, Bjoern

...

-Evan Bollig Research Associate | Application Developer | User Support Consultant Minnesota Supercomputing Institute 599 Walter Library 612 624 1447 evan@msi.umn.edu boll0107@umn.edu ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/