Hi Bernado,

can you try to change your $HOME/shed_tools to a full path?
Also please try my small tutorial here:

https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox

Hope that will help you!

Cheers - Bjoern

Am 08.04.2014 23:39, schrieb Bernardo Bello:

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&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)}'

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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/