"When available, install externally managed dependencies (e.g. conda)? Beta" is nowhere to be found. How to fix?

Question: "When available, install externally managed dependencies (e.g. conda)? Beta" is nowhere to be found. How to fix?

7 months ago by

mdgronke • 10

mdgronke • 10 wrote:

I believe I'm running the latest version of Galaxy Project, as I installed it from the site last week, so version 18,01

I am trying to install Trimmomatic from the Tool Shed. I get the message that: "This repository defines tool requirements that cannot be installed through the Tool Shed.Please activate Conda dependency resolution, etc."

As I understand it, Conda resolution is enabled by default, and I have not changed any of the settings. So it should run by default, no?

Also, I have read that I am supposed to have a button that says: "When available, install externally managed dependencies (e.g. conda)? Beta", however I do not see this check box anywhere on my screen when I try to install Trimmomatic via the tool shed.

How can I resolve this issue? Thanks.

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modified 7 months ago • written 7 months ago by mdgronke • 10

7 months ago by

mdgronke • 10

mdgronke • 10 wrote:

I figured out the problem. I did not have bzip2 installed, which meant the conda install did not properly work.

It was shown here when I deleted the _conda/ folder and tried re-running run.sh.

galaxy.tools.deps.conda_util INFO 2018-04-06 15:32:19,516 Installing conda, this may take several minutes. % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 54.9M 100 54.9M 0 0 23.2M 0 0:00:02 0:00:02 --:--:-- 23.2M WARNING: bzip2 does not appear to be installed this may cause problems below PREFIX=/usr/local/apps/galaxy/database/dependencies/_conda /tmp/conda_installxjJyGA.sh: line 333: bunzip2: command not found

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