Question: Error: You must set the environmental variable TRINITY_BASE_DIR to the base installation directory of Trinity before running this
0
gravatar for devbt15
20 days ago by
devbt1530
devbt1530 wrote:

Dear all,

While using trinityrnaseq_protocol, I have encountered the error (as described in the title of the question). I am running local galaxy from the bash terminal for Ubuntu on my windows PC. Please help. Unfortunately, this question was raised on Biostars but has not been answered yet: https://www.biostars.org/p/211070/ I also tried to report it using local galaxy but was not successful.

Thank you,

Dr. Debatosh Das,

Post-Doc (University of Munich),

Germany.

trinity rna-seq local galaxy • 120 views
ADD COMMENTlink modified 12 days ago • written 20 days ago by devbt1530
1
gravatar for Jennifer Hillman Jackson
12 days ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

There are a several Trinity repositories in the Main Tool Shed. This one you reference is older (from 2015). Specifically, the dependency to add this environment variable (see __add_to_PATH_setting.txt file) seems to have problems. It is not clear if this is an incompatibility between the repo version and the latest Galaxy versions.

The IUC owned Trinity tool versions are considered the most current and would be a good choice as an alternative, for example:

Trinity has been undergoing upgrades and changes since last spring. There are still some open issues associated with the IUC versions. Review here if you run into problems:

This particular problem is not reported in the above search, most likely since the error is only associated with the older repo's tools and that development repository, if a public version at Github or elsewhere even exists (it is not linked - it is optional metadata for a published repo).

The newer Trinity repositories do not include the same tool wrappers/version as older workflow protocol, however, most of those related tools are wrapped for Galaxy in other repositories. Trying to replicate that older workflow using the newer tool versions would be one possible solution. Setting this env variable directly yourself is another if you can determine how that is done using the info contained in the repository files. And contacting the repository owners through the Tool Shed is yet another and might be worth doing even if you choose to try one or both of the above. They might be able to help with fixing the install if they choose to still support this repo and you still prefer to use it.

To contact a repository owner, log into the Tool Shed at https://usegalaxy.org/toolshed, creating an account first if needed. Then navigate to the repo, click into one of the tools, and use the contact option in the upper right "Repository Actions" menu. This will send your message to the owners and ideally they would provide some feedback about this repo's status.

Tool Shed repositories are often created, owned, and maintained by the wider community. Not all will be supported/useable through time as Galaxy is upgraded unless the owners also make changes. How dependency installation is managed changed early this year and could be a factor. Most of the tools written by the core devteam and iuc owners have been upgraded or are in the process of being upgraded to address this same issue (dependency installation upgrades).

I will backlink in the prior question to this one. At the time it was asked, much was in flux as tools and Galaxy itself were being upgraded to the newer dependency handling. We didn't have an answer and knew that many tool authors were waiting for the dependency install changes to be finalized before investing in upgrading older tool repositories. This isn't a direct answer either for how to correct the problem, but instead advice about how to proceed now that the dependency resolution changes are mostly completed in the latest Galaxy/Tool Shed releases (some tuning is still occurring to fix minor issues as they are discovered).

Hopefully one of the above options works out for you! Jen, Galaxy team

ADD COMMENTlink modified 12 days ago • written 12 days ago by Jennifer Hillman Jackson23k
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