Hello Curt,
I believe that version 1.0.3 of the rpy package should be installing
successfully from the main tool shed if you have a repository that contains a
tool that defines a dependency to the rpy repository owned by devteam at
http://toolshed.g2.bx.psu.edu/view/devteam/package_rpy_1_0_3
Here is the last test run for the tool shed's install and test framework for
that repository. I believe tis should install correctly using the dist
repository, but if you're seeing problems, let us know. Also, the next release
is coming soon ( tentatively a week or so from now )..
Test runs
2014-04-07 17:25:49
Automated test environment
Successful installations
Repository dependencies - installation of these additional repositories is
required
Tool shed NameOwner Changeset revision
toolshed.g2.bx.psu.edu package_r_2_11_0devteam 5824d2b3bc8b
Tool dependencies
TypeNameVersion
R package 2.11.0
Installation directory
/ToolDepsMain/R/2.11.0/devteam/package_rpy_1_0_3/82170c94ca7c
TypeNameVersion
rpy package 1.0.3
Installation directory
/ToolDepsMain/rpy/1.0.3/devteam/package_rpy_1_0_3/82170c94ca7c
On Apr 8, 2014, at 3:28 PM, Hayes, Curt curt.ha...@seattlechildrens.org
wrote:
Hi there all,
Does anyone have RPY working? I install via toolshed and the folder is empty,
and shows missing dependencies.
I have searched previous posts, nothing since 2010. I have a local install
(production config – postgres, etc – on CENTOS 6.5). I posted last week and
it fell off the list.
From Galaxy User interface:
Dataset generation errors
Dataset 81: Build base quality distribution on data 9
Tool execution generated the following error message:
Traceback (most recent call last):
File
/apps/galaxy/galaxy-dist/tools/metag_tools/short_reads_figure_score.py,
line 12, in module
from rpy import *
ImportError: No module named rpy
I have attempted to download/install the scripts but they fail with multiple
errors (most posts out there have a bad URL) -
http://getgalaxyp.org/install.html says use:
curlhttp://rpy.svn.sourceforge.net/viewvc/rpy/trunk/rpy/?view=tar rpy.tar.gz
if you view that it redirects you to another URL.
Via shell: R is installed: R version 2.13.0 (2011-04-13)
Can someone provide me some help please to get it working via Galaxy? I
understand it works in Central.
From Toolshed:
Name
Version
Type
Installation status
rpy
1.0.3
package
Error
Toolshed Error:
In file included from src/rpymodule2110.c:51: src/RPy.h:56:20: error:
Python.h: No such file or directory In file included from
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:68,
from
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/arrayobject.h:14,
from src/RPy.h:89, from src/rpymodule2110.c:51:
/usr/lib64/python2.6/site-packages/numpy/core/include/numpy/npy_common.h:79:2:
error: #error Must use Python with unicode enabled. truncated
Thanks,
Curt
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