Question: Internal Server Error for workflow

2.4 years ago by

Hello

I am getting following error when I try to run the workflow from my admin account. my link is : http://localhost:8080/root?workflow_id=f2db41e1fa331b3e

Internal Server Error Galaxy was unable to successfully complete your request

An error occurred. This may be an intermittent problem due to load or other unpredictable factors, reloading the page may address the problem.

The error has been logged to our team.

Backend has below error: AttributeError: 'NoneType' object has no attribute 'valid_input_states'

Does anybody know about this problem?

Thanks Snehal

galaxy workflows • 994 views

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modified 2.3 years ago • written 2.4 years ago by snehalbpatil87 • 30

2.4 years ago by

Dannon Baker ♦ 3.7k

United States

Dannon Baker ♦ 3.7k wrote:

What galaxy version are you running?

ADD COMMENT • link written 2.4 years ago by Dannon Baker ♦ 3.7k

2.4 years ago by

snehalbpatil87 • 30

snehalbpatil87 • 30 wrote:

galaxy version is v 16.04..

My workflow is input --> bowtie(custom version) --> sam_to_bam-->samtools sort

ADD COMMENT • link modified 2.4 years ago • written 2.4 years ago by snehalbpatil87 • 30

2.4 years ago by

Dannon Baker ♦ 3.7k

United States

Dannon Baker ♦ 3.7k wrote:

I don't think you're running the 16.04 release if you're getting this error -- it wasn't introduced until after the 16.04 branch (so it only affected dev). You may want to double check your local repository state.

That said, this error has been fixed as of https://github.com/galaxyproject/galaxy/pull/2540, so updating should resolve your problems locally.

ADD COMMENT • link written 2.4 years ago by Dannon Baker ♦ 3.7k

2.4 years ago by

snehalbpatil87 • 30

snehalbpatil87 • 30 wrote:

Hello Dannon:

When I run git tag command it returned v16.04 and git pull returns :

Warning: Permanently added the RSA host key for IP address '**' to the list of known hosts. Already up-to-date..

Am I missing something?

ADD COMMENT • link written 2.4 years ago by snehalbpatil87 • 30

Try checking the output of 'git status'?

ADD REPLY • link written 2.4 years ago by Dannon Baker ♦ 3.7k

THis was the output of my git status

On branch dev

Changed but not updated:

(use "git add/rm <file>..." to update what will be committed)

(use "git checkout -- <file>..." to discard changes in working directory)

deleted: config/galaxy.ini.sample

deleted: config/tool_conf.xml.main

deleted: config/tool_data_table_conf.xml.sample

deleted: config/tool_shed.ini.sample

deleted: config/tool_sheds_conf.xml.sample

modified: tool-data/all_fasta.loc.sample

Untracked files:

(use "git add <file>..." to include in what will be committed)

.venv_old/

database/dependencies/

tools/mnuti/

tools/pullali/

tools/pullsam/

no changes added to commit (use "git add" and/or "git commit -a")

ADD REPLY • link written 2.4 years ago by snehalbpatil87 • 30

Ok, so you're definitely on the dev branch. If you want to stay on this branch, so you could do a 'git pull' to update. If you would like to check out a stable branch, you might want to do 'git checkout -b master origin/master' to stay on the permanent master branch.

Lastly, and it's a side issue, but you probably shouldn't delete those .sample files as updates will continue to show up in them as new options are added.

ADD REPLY • link written 2.4 years ago by Dannon Baker ♦ 3.7k

2.4 years ago by

snehalbpatil87 • 30

snehalbpatil87 • 30 wrote:

Hello Dannon: I follwed fork method beccause I am creating many custom workflows and tools in Galaxy. git pull gives me Already up-to-date message. But still I am having same workflow internal error problem.

ADD COMMENT • link written 2.4 years ago by snehalbpatil87 • 30

Ahh, so you forked Galaxy and have cloned from there? In that case, you'll need to update your fork, or pull from the main Galaxy repository specifically.

ADD REPLY • link written 2.3 years ago by Dannon Baker ♦ 3.7k

2.3 years ago by

snehalbpatil87 • 30

snehalbpatil87 • 30 wrote:

Hello Dannon:

I followed these steps to fork and clone galaxy repository. its pretty recent just a week old. https://help.github.com/articles/fork-a-repo/

Can there be any explanation for workflow problem?

Thanks Snehal

ADD COMMENT • link written 2.3 years ago by snehalbpatil87 • 30

Can you give me the output of 'git rev-parse HEAD' from the server's repository?

ADD REPLY • link written 2.3 years ago by Dannon Baker ♦ 3.7k

dd12980777181092984b16c786ed1eaf3aafa08b

ADD REPLY • link modified 2.3 years ago • written 2.3 years ago by snehalbpatil87 • 30

2.3 years ago by

snehalbpatil87 • 30

snehalbpatil87 • 30 wrote:

Hello Dannon:

Did you get chance to check on the version I have? Is there any tutorial on how to fork and clone it galaxy repository ?

Thanks Snehal

ADD COMMENT • link written 2.3 years ago by snehalbpatil87 • 30

Hey, yes, I would not manage your own fork for a production instance. Try these instructions here, to get the stable version of Galaxy: https://wiki.galaxyproject.org/Admin/GetGalaxy#Get_the_Code

Edit: And I did check out that changeset, and you should be on an up-to-date dev version. Like I mentioned, though, I'd probably track one of the stable releases, and not dev.

ADD REPLY • link modified 2.3 years ago • written 2.3 years ago by Dannon Baker ♦ 3.7k

But If I directly clone the repository, how will I keep different copy of my changes and get updates from main repository?

ADD REPLY • link written 2.3 years ago by snehalbpatil87 • 30

If what you're doing is mainly writing tools, I would not commit those to your galaxy codebase. I'd store them in a separate repository, and simply configure galaxy to use tools in that repository.

ADD REPLY • link written 2.3 years ago by Dannon Baker ♦ 3.7k

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On branch dev

Changed but not updated:

(use "git add/rm <file>..." to update what will be committed)

(use "git checkout -- <file>..." to discard changes in working directory)

deleted: config/galaxy.ini.sample

deleted: config/tool_conf.xml.main

deleted: config/tool_data_table_conf.xml.sample

deleted: config/tool_shed.ini.sample

deleted: config/tool_sheds_conf.xml.sample

modified: tool-data/all_fasta.loc.sample

Untracked files:

(use "git add <file>..." to include in what will be committed)

.venv_old/

database/dependencies/

tools/mnuti/

tools/pullali/

tools/pullsam/

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