Question: Galaxy instance in a pre-configured enviroment
gravatar for merella.stefania
2.7 years ago by
merella.stefania0 wrote:

Dear all, I am new of galaxy and I think that it is a great platform, so many thanks for the very good job.

I am trying to configure an instance of galaxy in our server that it is already configured with all the software for our sequencing analysis, like for example BWA, PICARD, bedtools, samtools etc. Meaning that I have not need to install the tools via repository using the admin interface because they are already in my machine.

Looking at the tutorials available in the web site, it seems that I have to add one by one my tools as if they were custom tools. Is that correct? Is there an easier way to do that? For example forcing galaxy to use the my local bin directory as repository. I searched a lot but I did not find anything, so sorry if this question was already asked.

Thanks again,


admin galaxy tools • 735 views
ADD COMMENTlink modified 2.7 years ago by Jennifer Hillman Jackson25k • written 2.7 years ago by merella.stefania0
gravatar for Jennifer Hillman Jackson
2.7 years ago by
United States
Jennifer Hillman Jackson25k wrote:


Using the Admin UI is the most direct option for a pre-existing Galaxy instance. You should be able to browse the Tool Shed and install each with a few clicks. Use managed dependencies whenever offered.

This is the Admin wiki, which it sounds like you have already found:

However, I want to make sure that you know about this specific subsection, since it has instructions for how to reorganized tools (once installed) into labeled groups in the Tool Panel. See the last section of:

Others are welcome to post more help/tips.

Thanks, Jen, Galaxy team

ADD COMMENTlink written 2.7 years ago by Jennifer Hillman Jackson25k

Hi Jen, Thanks for the answer. I don't have a pre-existing Galaxy instance. The Galaxy instance is new, I have a preconfigured environment meaning that the tools were installed before and independently the installation of Galaxy. So from your answer is not clear to me if, in any case, I simply have to use the UI and install tools. Does Galaxy read from /usr/local/bin directory?

Thanks for the kind support and again congrats for the great job!


ADD REPLYlink written 2.7 years ago by merella.stefania0

Hi Stefania

Yes, Galaxy (or rather the 'user' the Galaxy server is running as) can read from /usr/local/bin or any directory, as long it is in its path. Set up the environment variable accordingly, or add extra path information at the beginning of the script.

As a more general comment on your original question: Based on our own experience, I do not recommend to use the pre-configured tools. Our local Galaxy installation runs on a server with a lot of binaries/scripts/databases/indices/etc available (ie they are synced from another server). Original most of our tools relied on those. But we were running into several troubles like: a binary was upgraded to a different version and as a consequence, the Galaxy tool was no longer working.

Over time, we built a second software and database tree (with proper versioning) just used by Galaxy. This way, we might lag behind, but it guarantees reproducibility. And in recent years, we rely more and more on the tools and their dependencies from the tool shed.


ADD REPLYlink written 2.7 years ago by Hotz, Hans-Rudolf1.8k

Hi Hans, thank you so much for the great explanation. I will follow your suggestions. Really appreciate that.


ADD REPLYlink written 2.7 years ago by merella.stefania0
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