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 Name Owner Changeset revision toolshed.g2.bx.psu.edu package_r_2_11_0 devteam 5824d2b3bc8b Tool dependencies Type Name Version R package 2.11.0 Installation directory /ToolDepsMain/R/2.11.0/devteam/package_rpy_1_0_3/82170c94ca7c Type Name Version 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.hayes@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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