I am having great difficulty installing rpy (v1.0.3) for our local Galaxy installation. Is rpy actually supported for Galaxy? Should I even bother trying to install rpy?
David Hoover Helix Systems Staff http://helix.nih.gov
On Tue, Nov 16, 2010 at 7:45 PM, David Hoover hooverdm@helix.nih.gov wrote:
I am having great difficulty installing rpy (v1.0.3) for our local Galaxy installation. Is rpy actually supported for Galaxy? Should I even bother trying to install rpy?
Galaxy currently does use rpy (v1) in some tools. There is a bug open to upgrade to rpy2 (the API changed), http://bitbucket.org/galaxy/galaxy-central/issue/103/upgrade-rpy-to-latest-v...
I suggest you ask on the rpy mailing list, or post more details about what is going wrong with the installation or rpy.
Peter
At some point, we need to rewrite all the existing rpy tools for rpy 2 but right now, rpy 1.03 is something of a necessary wart:
[galaxy@q galaxy]$ grep rpy tools/*/*.py tools/metag_tools/short_reads_figure_high_quality_length.py:from rpy import * tools/metag_tools/short_reads_figure_score.py:from rpy import * tools/multivariate_stats/cca.py:from rpy import * tools/multivariate_stats/kcca.py:from rpy import * tools/multivariate_stats/kpca.py:from rpy import * tools/multivariate_stats/pca.py:from rpy import * tools/ngs_simulation/ngs_simulation.py:from rpy import * tools/plotting/histogram.py:from rpy import * tools/plotting/scatterplot.py:from rpy import * tools/regVariation/best_regression_subsets.py:from rpy import * tools/regVariation/linear_regression.py:from rpy import * tools/regVariation/rcve.py:from rpy import * tools/stats/cor.py:from rpy import * tools/stats/grouping.py:from rpy import * tools/stats/gsummary.py:from rpy import * tools/taxonomy/poisson2test.py:from rpy import *
Specifically, what problem are you having compiling rpy 1.03? I seem to remember having to hack part of it to recognize R version strings with 2 decimal places...
On Tue, Nov 16, 2010 at 2:45 PM, David Hoover hooverdm@helix.nih.govwrote:
I am having great difficulty installing rpy (v1.0.3) for our local Galaxy installation. Is rpy actually supported for Galaxy? Should I even bother trying to install rpy?
David Hoover Helix Systems Staff http://helix.nih.gov _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
David Hoover wrote:
I am having great difficulty installing rpy (v1.0.3) for our local Galaxy installation. Is rpy actually supported for Galaxy? Should I even bother trying to install rpy?
Hi David,
Yes, many of the tools in Galaxy still use rpy. It has not been updated for recent versions of R, but still works with them with a few modifications. These are:
Line 77 of src/RPy.h, remove the include of <Rdevices.h>.
Line 101 of rpy_tools.py, modify the version string regexp to:
" +([0-9].[0-9]+.[0-9])"
If you encounter additional problems after making these changes, please provide specific error messages.
Progress is being made to migrate tools away from rpy to rpy2 or standalone R scripts, but this has not yet been completed.
Thanks, --nate
David Hoover Helix Systems Staff http://helix.nih.gov _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Hi Nate,
I was able to get R version 2.6 to install with rpy-1.0.3, with a lot of warnings. Is a later version of R (2.10, 2.11, 2.12) absolutely required?
--David
On Nov 16, 2010, at 3:00 PM, Nate Coraor wrote:
Yes, many of the tools in Galaxy still use rpy. It has not been updated for recent versions of R, but still works with them with a few modifications.
David Hoover wrote:
Hi Nate,
I was able to get R version 2.6 to install with rpy-1.0.3, with a lot of warnings. Is a later version of R (2.10, 2.11, 2.12) absolutely required?
Probably not, although depending on which tools you want to use, you may also end up having to install old versions of the dependent modules.
--nate
--David
On Nov 16, 2010, at 3:00 PM, Nate Coraor wrote:
Yes, many of the tools in Galaxy still use rpy. It has not been updated for recent versions of R, but still works with them with a few modifications.
Anyway, I was able to install rpy-1.0.3 with R-2.12.0 by following your advice about the two edits. Thanks Nate!
David
On Nov 16, 2010, at 4:51 PM, Nate Coraor wrote:
David Hoover wrote:
Hi Nate,
I was able to get R version 2.6 to install with rpy-1.0.3, with a lot of warnings. Is a later version of R (2.10, 2.11, 2.12) absolutely required?
Probably not, although depending on which tools you want to use, you may also end up having to install old versions of the dependent modules.
--nate
--David
On Nov 16, 2010, at 3:00 PM, Nate Coraor wrote:
Yes, many of the tools in Galaxy still use rpy. It has not been updated for recent versions of R, but still works with them with a few modifications.
OK, I think I have everything installed. However, when I try to run Histogram or Scatterplot, I get the error
global name 'array' is not defined
This traces back to the ~/tools/plotting/histogram.py and scatterplot.py scripts. Is there something I'm missing?
David
On Nov 16, 2010, at 4:51 PM, Nate Coraor wrote:
David Hoover wrote:
Hi Nate,
I was able to get R version 2.6 to install with rpy-1.0.3, with a lot of warnings. Is a later version of R (2.10, 2.11, 2.12) absolutely required?
Probably not, although depending on which tools you want to use, you may also end up having to install old versions of the dependent modules.
--nate
--David
On Nov 16, 2010, at 3:00 PM, Nate Coraor wrote:
Yes, many of the tools in Galaxy still use rpy. It has not been updated for recent versions of R, but still works with them with a few modifications.
galaxy-dev@lists.galaxyproject.org
-
David Hoover -
Nate Coraor -
Peter -
Ross