Question: Tool dependencies, how to set the value of tool dependencies
gravatar for reubenmcgregor88
2.2 years ago by
reubenmcgregor8850 wrote:

Hi I have just managed to install a local version of galaxy and install it and set myself up as the Admin. I have very limited command line experience so this was a big step for me ;-)

I am now trying to install a tool on toolshed and have found it on the main toolshed.

However when I get to the install page I get the following essage:

"Tool dependencies defined in this repository can be automatically installed if you set the value of your tool_dependency_dir setting in your Galaxy config file (galaxy.ini) and restart your Galaxy server before installing the repository."

and can not check the box :Handle tool dependencies?

How do I "set the value of my tool_dependency_dir etcetc as suggested?

Or can I ingore this and hit the install button?


ADD COMMENTlink modified 2.2 years ago by Jennifer Hillman Jackson25k • written 2.2 years ago by reubenmcgregor8850
gravatar for Jennifer Hillman Jackson
2.2 years ago by
United States
Jennifer Hillman Jackson25k wrote:


tool_dependency_dir is set in the config/galaxy.ini file. Help:

You can install tools without it, but they will be missing components needed to execute the tools. If you want to install and configure these yourself, that is a choice, but it can be tedious unless (and even if!) you are an experienced administrator.

Thanks, Jen, Galaxy team

ADD COMMENTlink modified 2.2 years ago • written 2.2 years ago by Jennifer Hillman Jackson25k

Hi again Jen,

Sorry I've been asking so many questions, real rookie.

On the link it again states "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 config/galaxy.ini to a path writable by the Galaxy server."

I know it says "simply necessary" but I still don't know how to "set the tool_dependency_dir option of config/galaxy.ini to a path writable by the Galaxy server" in terminal... I know it's probably second nature to most. But I have simply been copy pasting command lines up to now from the website.

Thanks again


ADD REPLYlink written 2.2 years ago by reubenmcgregor8850

The commands that change/assign admin email are very similar to what you would do this for this one. This tutorial has a walk-through: Wherever you see universe_wgsi.ini in this older wiki - replace with config/galaxy.ini (the new name and location).

In short:

  1. First, decide where this directory will be. Capture the full path.

  2. Use grep against this line in the galaxy.ini file to find out what the line currently contains.

  3. Modify the admin "sed" command to change the default setting 1) remove the hash "#" at the start of the line and 2) include the directory path decided in #1.

Note: Since you already have a galaxy.ini file at this point, you will not be modifying the galaxy.ini.sample file and writing to galaxy.ini. Instead, modify the existing galaxy.ini file and output to a temporary file - you can name it anything you want. Grep again on the line in the temporary file to make sure it contains the expected content. When confirmed to be what you want, move ("mv") this temp file to galaxy.ini (overwriting it).

It is difficult to write up the exact line commands for each operation since so much is variable. If there is anyone you work with that has any line command experience at all, they will know how to do this. You can also google the terms "grep", "mv", "sed" and others - there is much help on the internet that includes examples (the terms have help built-in on the terminal, but those can be difficult to decipher for brand-new users). Knowing how to do these basic unix commands are really essential anyone doing bioinformatics to learn and not just when running a local Galaxy. Much can be automated, but little bits of tuning on the command-line will almost always be required when dealing with files and tools.

That said, I'll think about adding a section for doing this with exact instructions. My concern is that it may have very specific utility, creating more problems and confusion that it solves.

ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by Jennifer Hillman Jackson25k

Hi Jen,

I reached out to a friend who has used python a lot. And we managed to set the directory and edit the galaxy.ini file. I'm pretty sure it worked because I can now check the "Handle tool dependencies?" box.

However now when I trey to install any tool I get an error message: please see pictures (basically a bog red cross saying error as status)



However it states "see the Repository installation error below"but I can not see any error?

Please help, does it have anything to do with:

Shed tool configuration file:

Your Galaxy instance is configured with 1 shed-related tool configuration file, so repositories will be installed using its tool_path setting.??


Reuben p.s. I have noticed that the terminal is just repeating: - - [03/Oct/2016:22:33:40 +0100] "GET /admin_toolshed/manage_repository?id=f2db41e1fa331b3e HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_12) AppleWebKit/602.1.50 (KHTML, like Gecko) Version/10.0 Safari/602.1.50"

in the background, why is it mentioning mozilla? I am using safari...

ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by reubenmcgregor8850
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