Question: Get Galaxy Tool Shed Work On Local Instance
1
gravatar for biotech
4.9 years ago by
biotech510
United States
biotech510 wrote:

Hi,

I am having problems to install tools from tool shed. 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.

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

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

Thanks, Bernardo

P.S. I also posted this in Galaxy-dev mailing list.

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
done # 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

done # 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

done # 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)

done # Then, I created a shed_tools folder in my $HOME directory before modifying the shed_tool_conf.xml file

<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)}'
galaxy • 4.7k views
ADD COMMENTlink modified 4.9 years ago by Björn650 • written 4.9 years ago by biotech510
1

The minimum things needed for tool from the Tool Shed instalation to work are described here: https://wiki.galaxyproject.org/Admin/Tools/AddToolFromToolShedTutorial You don't need to do anything with tool_config_file, tool_path, shed_tool_conf.xml or R manually for a basic installation. For troubleshooting purposes I would try to omit these steps.

Deep insights into repository management are provided here: https://wiki.galaxyproject.org/InstallingRepositories

Also can you please post the full line from your config that starts tool_dependency_dir ?

ADD REPLYlink modified 4.9 years ago • written 4.9 years ago by martenson380

Thanks emulatorer, I finally reinstalled Galaxy with Bjoern tutorial and is woking now. I installed R packages because S-MART seems to need them. I though it was this way, as they indicate in their tool.

ADD REPLYlink written 4.9 years ago by biotech510

You are right, if the tool declares it you should probably install it. Maybe in the future tool author will manage the tool dependencies through toolshed to save users from doing this (and using root).

ADD REPLYlink written 4.9 years ago by martenson380
1
gravatar for Björn
4.9 years ago by
Björn650
Germany
Björn650 wrote:

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

ADD COMMENTlink written 4.9 years ago by Björn650
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