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.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 > > CONFIDENTIALITY NOTICE: This e-mail message, including any attachments, is > for the sole use of the intended recipient(s) and may contain confidential > and privileged information protected by law. Any unauthorized review, use, > disclosure or distribution is prohibited. If you are not the intended > recipient, please contact the sender by reply e-mail and destroy all copies > of the original message. > ___________________________________________________________ > 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/
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