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

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

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

done # Go to http://localhost:8080/ and register as popn...@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

admin_users = popn...@gmail.com

# Set 'Tool 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. #

# 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("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)}'


*Bernardo Bello Ortí*

PhD student


Campus de Bellaterra-Universitat Autònoma de Barcelona

Edifici CReSA

08193  Bellaterra (Barcelona, Spain)

Tel.: 647 42 52 63 *www.cresa.es <http://www.cresa.es>  *
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