Hi,
I am having problems to install a tool from tool shed named S_MART on my local Galaxy. In fact, its the first tool I'm trying to install. The reason to install S-MART is to use DETR'PROK in Galaxy.
Here is the 'error' Galaxy shows after installing some programs from toolshed.https://drive.google.com/file/d/0B8-ZAuZe8jldN3ptYzE5N0p2ZGM/edit?usp=sharing
I've seen this related post, but I don't know if we are talking about the same problem.http://dev.list.galaxyproject.org/Problem-installing-tool-Galaxy-local-td4662775.html
Here are the commands aI've used up to now:
Thanks, Bernardo
P.S. Sorry for the duplicated email, I mistyped the subject in the previous one.
hg clone https://bitbucket.org/galaxy/galaxy-dist/ cd galaxy-dist hg update stable
sh run.sh # gave errors, so see below
# solve problem at startup ( https://www.mail-archive.com/galaxy-dev@lists.bx.psu.edu/msg13354.html) % export LC_ALL='en_US.UTF-8' % sh run.sh
done # Go to http://localhost:8080/ and register as popnard@gmail.com # Setup admin user (https://wiki.galaxyproject.org/Admin/Interface). To give a user Galaxy admin privileges, add their Galaxy login ( email ) to the list in the following config setting in the Galaxy configuration file universe_wsgi.ini.
admin_users = popnard@gmail.com
# Set 'Tool Dependencies' https://wiki.galaxyproject.org/Admin/Config/ToolDependencies?action=show&... mkdir tool_dependency_dir
done # add tool dependencies folder to 'universe_wsgi.ini' -> Galaxy provides a method for managing the dependencies of Galaxy tools installed from the Tool Shed. In this case, it is simply necessary to set the tool_dependency_dir option of universe_wsgi.ini to a path writable by the Galaxy server.
done # restart server
First, I modified the universe_wsgi.ini file by removing the "#" before the tool_config_file and tool_path lines. # http://user.list.galaxyproject.org/Installing-new-tools-from-the-tool-shed-t...
# Then, I created a shed_tools folder in my $HOME directory before modifying the shed_tool_conf.xml file <?xml version="1.0"?> <toolbox tool_path="$HOME/shed_tools"> </toolbox>
done # INSTALL R done # ADD R PACKAGES R --slave --no-save --no-restore --quiet -e 'if("RColorBrewer" %in% rownames(installed.packages()) == FALSE){install.packages("RColorBrewer", repos = c("http://cran.rstudio.com/"), dependencies = TRUE)}' R --slave --no-save --no-restore --quiet -e 'if("Hmisc" %in% rownames(installed.packages()) == FALSE){install.packages("Hmisc", repos = c("http://cran.rstudio.com/"), dependencies = TRUE)}'