Flexynesis tool failure - mkdir: mkdir: cannot create directory 'tmp': Permission denied error

1

mkdir: mkdir: cannot create directory ‘tmp’: Permission denied

Server instance: UseGalaxy . eu

2

Hi @lordtsage

This message usually indicates a problem with the tool wrapper However, sometimes odd things such as empty or unreadable inputs can as well.

I’ll run a quick test to see if I can reproduce the issue with sample data. Which of the 5 tools was this happening with?

I would suggest quickly double checking your inputs, and if those look Ok, use the bug report icon to submit this to the local server administrators. You can include a link to this topic in the comments if you want to (this makes it easier them to comment back here).

If you want to share back the full error job for feedback, we can do the initial review together, too! I’ll start some tool tests up to see if I can find the issue but these will be mostly guesses without an example. :slight_smile:

3

Hi Jennaj,

I am working on the tutorial: Modeling Breast Cancer Subtypes with Flexynesis

I am following this step by step and I get the error when I attempt to train the model. Now, the error report also shows no bug icon, as you shall see, which makes my life very difficult..

Let me know if you need anything else.

4

Hi @lordtsage

Thanks, I am able to reproduce the issue with initial Galaxy tutorial as well. I’ve sent in an error report from the workflow invocation (the only way to currently technically report this).

I’ve bundled what you found with my findings in a ticket here. The older versions of the tool suite appear to have trouble unpacking the data from the AWS share, then the newer versions either still have that same issue (and it is failing higher up the chain) or there is some new issue with writing the unpacked outputs.

Let’s give the EU developers a chance to respond. If we don’t hear back from them by next week, we can ping them directly for an update then.

Thanks for the follow up! :hammer_and_wrench:

5

Hi @lordtsage

Which version of Flexynesis are you using?
Can you please share the history?

best,

Amirhossein

6

I am working on the website. I have attached a picture of the history

screenshot-1784835801628
screenshot-17848358016281908×882 185 KB

7

Hi @lordtsage

Can you please share me the history? here is the how to: FAQ: Sharing your History

8

Hi @nilchia Galaxy

9

Thanks for sharing the history @lordtsage !!

Hi @nilchia, the tool version is the most current. This is the same error I reported at Github (item 3).

My copy of the history with reruns:

Current version, fails with rerun today.

toolshed.g2.bx.psu.edu/repos/bgruening/flexynesis/flexynesis/1.1.11+galaxy0

Tutorial version (link to step). The job is still queued.

toolshed.g2.bx.psu.edu/repos/bgruening/flexynesis/flexynesis/1.1.10+galaxy0

10

Hi,

The problem is resolved. Please try again.

Best,

Amirhossein

11

sounds like from what Jennaj said, the writing error you’re hitting might actually be the newer version’s problem, different from the unpacking issue the older ones have. worth checking from that screenshot whether youre on the old or new release—that could help narrow down whats actually broken.