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.

I've seen this related post, but I don't know if we are talking about the same problem.

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&redirect=Admin%2FConfig%2FTool+Dependencies

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-td4655241.html

# 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)}'