Re: [galaxy-dev] package_r_2_11_0 and ggplot2

2014-07-31 Thread 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
e...@msi.umn.edu
boll0...@umn.edu


On Tue, Jul 29, 2014 at 4:22 PM, Björn Grüning
bjoern.gruen...@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_0.9.3.1.tar.gz

 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_dependencies/package_deseq2_1_2_10

 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
 e...@msi.umn.edu
 boll0...@umn.edu


 On Tue, Jul 29, 2014 at 2:46 PM, Björn Grüning
 bjoern.gruen...@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
 e...@msi.umn.edu
 boll0...@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/




___
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/

Re: [galaxy-dev] package_r_2_11_0 and ggplot2

2014-07-31 Thread Björn Grüning

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
e...@msi.umn.edu
boll0...@umn.edu


On Tue, Jul 29, 2014 at 4:22 PM, Björn Grüning
bjoern.gruen...@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_0.9.3.1.tar.gz

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_dependencies/package_deseq2_1_2_10

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
e...@msi.umn.edu
boll0...@umn.edu


On Tue, Jul 29, 2014 at 2:46 PM, Björn Grüning
bjoern.gruen...@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
e...@msi.umn.edu
boll0...@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/






___
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/

Re: [galaxy-dev] package_r_2_11_0 and ggplot2

2014-07-31 Thread Evan Bollig
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
e...@msi.umn.edu
boll0...@umn.edu


On Thu, Jul 31, 2014 at 1:51 PM, Björn Grüning
bjoern.gruen...@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
 e...@msi.umn.edu
 boll0...@umn.edu


 On Tue, Jul 29, 2014 at 4:22 PM, Björn Grüning
 bjoern.gruen...@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_0.9.3.1.tar.gz

 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_dependencies/package_deseq2_1_2_10

 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
 e...@msi.umn.edu
 boll0...@umn.edu


 On Tue, Jul 29, 2014 at 2:46 PM, Björn Grüning
 bjoern.gruen...@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
 e...@msi.umn.edu
 boll0...@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/





___
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/

Re: [galaxy-dev] package_r_2_11_0 and ggplot2

2014-07-29 Thread Björn Grüning

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
e...@msi.umn.edu
boll0...@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/


___
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/


Re: [galaxy-dev] package_r_2_11_0 and ggplot2

2014-07-29 Thread 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? 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
e...@msi.umn.edu
boll0...@umn.edu


On Tue, Jul 29, 2014 at 2:46 PM, Björn Grüning
bjoern.gruen...@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
 e...@msi.umn.edu
 boll0...@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/



___
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/

Re: [galaxy-dev] package_r_2_11_0 and ggplot2

2014-07-29 Thread Björn Grüning



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_0.9.3.1.tar.gz

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_dependencies/package_deseq2_1_2_10


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
e...@msi.umn.edu
boll0...@umn.edu


On Tue, Jul 29, 2014 at 2:46 PM, Björn Grüning
bjoern.gruen...@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
e...@msi.umn.edu
boll0...@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/




___
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/