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Question: Problem with installation GATK
0
gravatar for Noè
3.2 years ago by
Noè • 0
European Union
Noè • 0 wrote:

Hello,

I have tried to install NGS GATK tools but there is a problem with dependecies, because all are installed correctly only Package_picard_1_56_0 reports "Installed, missing tool dependencies".

What is the problem?

Thank you in advance for you help and attention!

 
gatk package picard missing tool dependencies • 1.0k views
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modified 3.2 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.2 years ago by Noè • 0
1
gravatar for Jennifer Hillman Jackson
3.2 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Installing tools with the checkbox for "manage dependencies" will likely solve this. Uninstalling then reinstalling is often the best way rather than installing each dependency individually, but that is also possible if needed (some tools do not have all dependencies set up for this function).

Before doing this, make sure the value in your config/galaxy.ini file for tool_dependency_dir is set to an existing directory that Galaxy can write to.

# Path to the directory in which tool dependencies are placed.  This is used by
# the tool shed to install dependencies and can also be used by administrators
# to manually install or link to dependencies.  For details, see:
#   https://wiki.galaxyproject.org/Admin/Config/ToolDependencies
# If this option is not set to a valid path, installing tools with dependencies
# from the Tool Shed will fail.
#tool_dependency_dir = None

After any changes, be sure to restart.

Thanks, Jen, Galaxy team
ADD COMMENT • link written 3.2 years ago by Jennifer Hillman Jackson ♦ 25k
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