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John Crow
@crowja
Thanks, I'll give it a try.
Nolan Woods
@innovate-invent
remember tool files have to follow xml encoding
John Crow
@crowja
@innovate-invent Thanks very very much Nolan!
Nolan Woods
@innovate-invent
:thumbsup:
Qiang Gu
@qiagu

Has anyone meet such kind of error?

alaxy.web.framework.decorators ERROR 2019-09-30 19:41:01,041 [p:26144,w:1,m:0] [uWSGIWorker1Core1] Uncaught exception in exposed API method:
Traceback (most recent call last):
  File "lib/galaxy/web/framework/decorators.py", line 283, in decorator
    rval = _format_return_as_json(rval, jsonp_callback, pretty=trans.debug)
  File "lib/galaxy/web/framework/decorators.py", line 316, in _format_return_as_json
    json = safe_dumps(rval, **dumps_kwargs)
  File "lib/galaxy/util/json.py", line 82, in safe_dumps
    dumped = json.dumps(obj, allow_nan=False, **kwargs)
  File "/usr/lib/python2.7/json/__init__.py", line 251, in dumps
    sort_keys=sort_keys, **kw).encode(obj)
  File "/usr/lib/python2.7/json/encoder.py", line 207, in encode
    chunks = self.iterencode(o, _one_shot=True)
  File "/usr/lib/python2.7/json/encoder.py", line 270, in iterencode
    return _iterencode(o, 0)
UnicodeDecodeError: 'utf8' codec can't decode byte 0x8b in position 5: invalid start byte

It happens when invoking a tool that contains tabluar input. Initial debugging shows that the issue seems to be related to tsv.gz datasets in history.

Nicola Soranzo
@nsoranzo
Looks like a Galaxy bug, can you open an issue please?
Qiang Gu
@qiagu
@nsoranzo Not always happen. Let me see whether I can reproduce the issue.
Nolan Woods
@innovate-invent
did the upload1 tool change?
{"err_msg": "Tool not found or not accessible.", "err_code": 0}
-----------------------------13003838246754604531405704901
Content-Disposition: form-data; name="history_id"

a799d38679e985db
-----------------------------13003838246754604531405704901
Content-Disposition: form-data; name="inputs"

{"file_count":1,"files_0|NAME":"stub.gbk","files_0|type":"upload_dataset","files_0|file_type":"genbank","files_0|dbkey":"?","dbkey":"?","file_type":"genbank","ajax_upload":"true"}
-----------------------------13003838246754604531405704901
Content-Disposition: form-data; name="tool_id"

upload1
-----------------------------13003838246754604531405704901
Content-Disposition: form-data; name="files_0|file_data"; filename="stub.gbk"
Content-Type: application/octet-stream


-----------------------------13003838246754604531405704901
Content-Disposition: form-data; name="key"

e0c5810725c4c1d1a805158846cacff8
-----------------------------13003838246754604531405704901--
I reinstall galaxy and suddenly it stops working :/
oh, even the Galaxy web interface fails to upload
Nolan Woods
@innovate-invent
has anyone seen Galaxy fail to locate its upload1 tool before?
Dannon
@dannon
gronke: sorry, I'm out today, missed that. Yes, using the text input w/ configfiles should do it I'd think.
@innovate-invent Sure haven't. Did you update since last time this worked?
Nolan Woods
@innovate-invent
I wonder if this is a python 3 thing
Nolan Woods
@innovate-invent
hm, upload1 isnt listed at /api/tools/
Nolan Woods
@innovate-invent
oh, ok.. something mangled my tool_conf
amiasjames
@amiasjames
Hello, I am trying to Run Galaxy Bridge on my local machine. I've manged to do this without issue but the tools i want to use, that come with Bridge, require the programs, Charmm and namd, to be installed separately, could anyone give me any tips on how to do this?
galaxybot
@galaxybot
[melichar] Hi, I want to implement s3 object storage into galaxy. I know that i need to modify object_store_conf.xml, but I also need to setup custom endpoint url. How and where can I do that?
John Crow
@crowja
In the xml for a tool, is it possible to specify a param and value without it requiring input from the user? This is more or less hardcoding a value.
Björn Grüning
@bgruening
@crowja you can either do this directly in the command section (e.g. --min -1) or as a type="hidden" param
John Crow
@crowja
@bgruening thanks! I think the hidden param is exactly what I need.
Jennifer Hillman-Jackson
@jennaj
Could someone more familiar with LADP/Galaxy interactions please help this user? https://help.galaxyproject.org/t/new-user-auto-creation-with-ldap-authentication-failing/2191
Chinmay Rele
@Dr-Drosophila
Does anyone use G-OnRamp? I need help signing up...
James Taylor
@jxtx
Ping @luke-c-sargent
luke
@luke-c-sargent
hello @Dr-Drosophila! How can I be of assistance
Chinmay Rele
@Dr-Drosophila

@luke-c-sargent

There is a link to a G-OnRamp instance in some documentation I am trying to follow. I am not able to go to it.

galaxybot
@galaxybot
[sargentl] I am guessing this is the Virtual Machine Image tutorial, as that’s an internal IP meant to redirect to a running virtual instance of G-OnRamp
Chinmay Rele
@Dr-Drosophila
No, I am trying to follow "Introduction to G-OnRamp Walkthrough" within the same directory, but the links are the same, and when I tried to follow what you sent, it didn't load either...
galaxybot
@galaxybot
[sargentl] ah, i see. the virtual machine installation portion is a pre-requisite, per the second paragraph of 1. Introduction:
We will use the G-OnRamp virtual machine for this walkthrough.[See the "Virtual Machine Installation Walkthrough" for instructions on how to install the virtualization software VirtualBox and the G-OnRamp virtual appliance.]
[sargentl] however, being able to access that document is a pretty important first step, let’s see about that
Chinmay Rele
@Dr-Drosophila
I am able to access all the documentation.. that is not the issue. The issue was following a link within the documentation you send. Apologies if that wasn't clear from my side
Do I need to have an AWS EC2 login in order to open a G-OnRamp VM?
luke
@luke-c-sargent
nope! it’s all local — that’s one of the main benefits of the VM, free to explore and muck about with
so, the link i posted above did not work for you, but you are otherwise able to access the tutorial "Virtual Machine Installation Walkthrough”?
Ultimately, you need to follow those steps to get a VM running; once you’ve done that, the 192.168.56.18 link will resolve to your locally-running VM of G-OnRamp
Chinmay Rele
@Dr-Drosophila
I am able to access the tutorial with and without the link you're provided.
alright. I will give it a try. thank you Luke :) So much better than Kenobi :D
luke
@luke-c-sargent
glad to be of service, may the Galaxy be with you ;) if you need anything else let me know, i’ll just be here tuning up my cantankerous droids
Chinmay Rele
@Dr-Drosophila
Instead of running a VM locally, can I instead run a VM on AWS EC2?
luke
@luke-c-sargent
you could use our AMI (Amazon Machine Image) — however, the links referring you to 192.168.56.18 would be invalid. You would use whatever IP Amazon assigns you (or your own, if you have a static IP to assign to it)
Chinmay Rele
@Dr-Drosophila
Alright. Do you suggest I run G-OnRamp locally, or using AWS? Assume I have minimal computing power locally.
luke
@luke-c-sargent
if you want to experiment and get a sense of how the system works and run some sample data, i would use the VM
then if you need more computational power for larger data sets, you can upgrade to AWS. it will incur charges proportional to the amount of power you request, however
unless ‘minimal computing power’ == totally unusable, then you could launch a smaller, cheaper instance for learning purposes on AWS
Chinmay Rele
@Dr-Drosophila
Is there documentation for how to get G-OnRamp up and running using AWS?
luke
@luke-c-sargent
indeed! the 'CloudLaunch Deployment Walkthrough’ is the easiest approach, though we also have a doc for doing it through AWS directly: https://ohsu.app.box.com/file/522085387090
(this hasn’t been put on the website quite yet, but i will do that presently)