Installing S-Mart on Mac SOX local instance

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Installing S-Mart on Mac SOX local instance

Bernardo Bello

I am having problems to install a tool from tool shed named S_MART on my local Galaxy.
The reason to install S_MART is to use DETR'PROK in Galaxy.

Attached is the 'error' Galaxy indicates after installing some programs from toolshed.

Here are the commands aI've used up to now:


cd galaxy-dist
hg update stable

sh # gave errors, so see below

% export LC_ALL='en_US.UTF-8'
% sh

done # Go to http://localhost:8080/ and register as [hidden email]
# Setup admin user ( 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 = [hidden email]

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. #

# 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">

done # INSTALL R
R --slave --no-save --no-restore --quiet -e 'if("RColorBrewer" %in% rownames(installed.packages()) == FALSE){install.packages("RColorBrewer", repos = c(""), dependencies = TRUE)}'
R --slave --no-save --no-restore --quiet -e 'if("Hmisc" %in% rownames(installed.packages()) == FALSE){install.packages("Hmisc", repos = c(""), dependencies = TRUE)}'


Bernardo Bello Ortí

PhD student


Campus de Bellaterra-Universitat Autònoma de Barcelona

Edifici CReSA

08193  Bellaterra (Barcelona, Spain)

Tel.: 647 42 52 63  

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