This thread is the designated place to ask questions about running the **hello_world** workflow.
Created by James Eddy jaeddy Hi everyone,
I have another problem when running the dockstore-tool-synapse-get.cwl:
Thanks for your help.
Cheers,
Thuc.
$ cwltool --non-strict dockstore-tool-synapse-get.cwl hello_world_get.cwl.json
it says:
SynapseHTTPError: 401 Client Error: Unauthorized
{"reason":"Timestamp in request, 2017-09-19T10:09:34.000Z, is out of date"} Thanks, Michael.
I see.
Cheers,
Thuc. Hi Thuc
I think the reason you got an error with "print", is your python 3.6. I don't think cwltool is supposed to be used in that Python version. Try to run the same in Python 2.7
Regards,
Michael Hi everyone,
When I run the synapse-get, it throws an error. Do you have any idea about the error?
Cheers,
Thuc.
(hello_world) INM274863:hello_world_run letd$ cwltool --non-strict dockstore-tool-synapse-get.cwl hello_world_get.cwl.json
Traceback (most recent call last):
File "/Users/letd/anaconda/bin/cwltool", line 7, in
from cwltool.main import main
File "/Users/letd/anaconda/lib/python3.6/site-packages/cwltool/main.py", line 472
print u"\nOptions for %s " % args.workflow
^
SyntaxError: Missing parentheses in call to 'print' Hi @byoo,
Two things:
1. You shouldn't need to use `dockstore-tool-helloworld.cwl` directly. This is the Dockerized *tool* that is used in the single step of the **hello_world** workflow. To run the workflow itself, you'll want to use `hello_world.cwl`.
2. When running the **hello_world** workflow described in `hello_world.cwl`, you should use the `hello_world.cwl.json` parameters file instead of the `hello_world_submit.cwl.json` file (which corresponds to `dockstore-tool-synapse-submit.cwl`).
To run the workflow, the command should look like this:
```
cwltool --tmpdir-prefix tmp/ --non-strict hello_world.cwl hello_world.cwl.json
```
You can check out the documentation wiki for **hello_world** [here](https://www.synapse.org/#!Synapse:syn9630940) for a complete example of how to run the workflow.
Let me know if you run into any other issues! Hello, I need help in submission; dockstore-tool-helloworld.cwl seem to expect a template file as a first argument. Thank you in advance!
Command:
```
cwltool --tmpdir-prefix tmp/ --non-strict dockstore-tool-helloworld.cwl hello_world_submit.cwl.json
```
Error log:
```
cwltool 1.0.20170817131858
Resolved 'dockstore-tool-helloworld.cwl' to 'file:///hello_world/dockstore-tool-helloworld.cwl'
dockstore-tool-helloworld.cwl:3:1: unrecognized extension field `http://purl.org/dc/terms/creator`. Did you include a $schemas section?
Workflow error, try again with --debug for more information:
Invalid job input record:
dockstore-tool-helloworld.cwl:28:3: Missing required input parameter `input_file`
~
```
dockstore-tool-helloworld.cwl:
```
...
inputs:
template_file:
type: File
inputBinding:
position: 1
input_file:
type: File
inputBinding:
position: 2
...
```
Benjamin;
Thanks much for reporting this and following up. I'm in agreement with James, don't use the `--cachedir` feature of cwltool as it often causes issues, so this makes sense with your outcomes. If you want workflow reuse on local runs, both Toil (http://toil.readthedocs.io) and Rabix Bunny (https://github.com/rabix/bunny) support them. Hope this get working cleanly now. Thanks for getting back to me I use:
cwltool 1.0.20170413194156
Also @chapmanb
Runs successfully if I just use the
```
--tmpdir-prefix
```
and exclude the
```
--cachedir
```
(see verified submission) Hi @benstory,
Which version of `cwltool` are you using? We've had some issues with the cache feature when attempting to run some other workflows as well ? my understanding is that this feature isn't entirely stable yet (cc @chapmanb). If you try to run with just `--tmpdir-prefix` argument, but not `--cachedir`, do you get a different result?
Running the tool with tmp and cache directories specified results in an error:
```
cwltool --tmpdir-prefix tmp/ --cachedir cache/ --non-strict hello_world.cwl hello_world.cwl.json
```
Example error:
```
[job dockstore-tool-synapse-get.cwl] completed success
Unhandled error, try again with --debug for more information:
[Errno 21] Is a directory: '/tmpdata/story/hello_world_run/cache/7f35629c0273214bab343a2ae5c888f0/synapse_files/hello_world_ref'
```
Running it without those two dir's specified works fine.
Hi Sourav,
There might have been an incompatibility between the example I was referencing when I first wrote the `dockstore-tool-synapse-submit` tool and some versions of `cwltool`. For `cwltool==1.0.20170217172322`, which we've used for most of the workflow testing here, I've been able to run both the `synapse-submit` tool as well as `dockstore-tool-synapse-get` by including the `--non-strict` flag ? e.g.:
```shell
cwltool --non-strict dockstore-tool-synapse-get.cwl hello_world_get.cwl.json
```
I just updated that in the documented example here: https://www.synapse.org/#!Synapse:syn9630940. Apologies for the confusion!
Depending on the version of cwltool you might need to use `--non-strict` option to ignore unrecognized fields in your workflow/tool. Is there something wrong with the cwltool installation? Hello,
While running the submission command using ``dockstore-tool-synapse-submit``, I get the following error:
```
Tool definition failed validation:
dockstore-tool-synapse-submit.cwl:3:1: Object `dockstore-tool-synapse-submit.cwl` is not valid
because
tried `CommandLineTool` but
unrecognized extension field
`http://purl.org/dc/terms/creator` and strict is True. Did
you include a $schemas section?
```