[galaxy-dev] API - Status 403 Forbidden

I'm trying to use the blend4j to access the Galaxy API, but I'm getting a 403 error, however when I pass the same request string through my browser I get a json response (Status 200). //Here is the URL string being passed in both cases: http://localhost:8080/api/histories?key=c5954f0e726e52da297cd

[galaxy-dev] BioBlend: Problem Running Example file

I had trouble running blend4j, so I tried to jump into python (a language I have little experience with). I tried running the example run_import_workflow.py *% python run_imported_workflow.py http://localhost:80808c25bc83f6f9e4001dd21eb7b64f063f * but I get an error: Initiating Galaxy connectio

Re: [galaxy-dev] API - Status 403 Forbidden

gt; without a browser session (perhaps from wget or curl) then I am > confident the blend4j part will work (or at least we can get it to). > > -John > > On Thu, Mar 7, 2013 at 9:09 PM, Rob Leclerc > wrote: > > I'm trying to use the blend4j to access the Galaxy API, but

Re: [galaxy-dev] BioBlend: Problem Running Example file

.macosx-10.6-intel/egg/simplejson/decoder.py", line 420, in raw_decode simplejson.decoder.JSONDecodeError: No JSON object could be decoded: line 1 column 0 (char 0) -Rob On Fri, Mar 8, 2013 at 11:23 AM, Sytchev, Ilya wrote: > JSONDecodeError will be raised if the given JSON document is not valid. > http:

Re: [galaxy-dev] BioBlend: Problem Running Example file

Dannon, *Thank you* you're absolutely right! ...Now I just have to deal with the permission denied errors. (The I set the galaxy admin to my userID/email). Cheers! Rob Rob Leclerc, PhD <http://www.linkedin.com/in/robleclerc> <https://twitter.com/#!/robleclerc> P: (US) +1

[galaxy-dev] example_watch_folder.py : URL did not return JSON data

I'm trying to get the example_watch_folder.py to work with a simple example, but I am running into an error (Caveat, python is not my native language) I call the following script, but get the subsequent error: $ ./example_watch_folder.py 8c25bc83f6f9e4001dd21eb7b64f063f http://localhost:8080/ /Us

Re: [galaxy-dev] example_watch_folder.py : URL did not return JSON data

I'm not familiar with python, but I can't see where 'library[0]['id']' is set or is in scope, since this seems to be the item in the iterator above this section. Cheers, Rob Rob Leclerc, PhD <http://www.linkedin.com/in/robleclerc> <https://twitter.com/

Re: [galaxy-dev] example_watch_folder.py : URL did not return JSON data

ou add (between 29 and 30) a 'print library' to see what that call > actually results in? > > Off the top of my head, this might be happening if your user account (that > the API key is associated with) isn't an admin account -- only admins can > create Data Libraries.

Re: [galaxy-dev] example_watch_folder.py : URL did not return JSON data

quot;: "file", "url": "/api/histories/2d9035b3fc152403/contents/81991b32733a4fc4" ] 9. You can navigate to the JSON description of the file in your browser: http://localhost:8080/api/histories/2d9035b3fc152403/contents/81991b32733a4fc4 and the output file

[galaxy-dev] Internal Server Error - Creating Workflows

If you create a Workflow and then try to access it through the API, https://main.g2.bx.psu.edu/api/workflows/ the server will emit a 500 Internal Server Error. Changing the output filename on the workflow and then saving seems to fix the issue. Cheers, Rob __

[galaxy-dev] example_watch_folder.py

If you're having problems with example_watch_folder.py you may need to increase the delay hack on line 55 to 15-20 seconds. Without the increased delay, it would upload a zerobyte file for me. It's not clear why, but there is a delay between the creation of a file name and the setting of the file

[galaxy-dev] Trouble Shooting example_watch_folder.py

ot;top200", "type": "file", "url": "/api/histories/2d9035b3fc152403/contents/81991b32733a4fc4" ] 10. You can navigate to the JSON description of the file in your browser: http://localhost:8080/api/histories/2d9035b3fc152403/contents/81

[galaxy-dev] Production Servers - Best Practices

AWS/CapacityPlanning> Using Amazon EBS Volumes <http://aws.amazon.com/ebs/> Copying an Amazon EBS Snapshot<http://docs.aws.amazon.com/AWSEC2/latest/UserGuide/ebs-copy-snapshot.html> ** Rob Leclerc, PhD <http://www.linkedin.com/in/robleclerc> <http

[galaxy-dev] Galaxy - FTP Download Problem

We have a CloudMan Galaxy install on Amazon and I'm able to upload FTP files from FireZilla (or programatically through a Java service I wrote). However, I'm unable to download that same file once uploaded. The 550 response is a "Requested action not take. File unavailable (e.g., file not found, n

[galaxy-dev] Setting up SSL on CloudMan EC2

Has anyone configured SSL for nginx on CloudMan (AWS)? If so, can you share your nginx.conf file as I'm having some issues. *Details* I tried adopting the nginx.conf for CloudMan+CloudBioLiniux as described here

[galaxy-dev] snpEff on Galaxy

at ca.mcgill.mcb.pcingola.vcf.VcfEntry.(VcfEntry.java:66) at ca.mcgill.mcb.pcingola.fileIterator.VcfFileIterator.parseVcfLine(VcfFileIterator.java:274) ... 8 more I'm going to assume that this is all related to the first issue, but I'm not sure how to fix the issue. Cheers

Re: [galaxy-dev] directory copies as zero-length file from job_working_directory?

Hi Nikhil, I've encountered this issue as well when using the API. Some scripts were using a 5 second sleep default to allow for copying the file to the output directory, but I found that I needed up to 15 seconds (occasionally that's not even enough). Cheers, Rob Rob Leclerc, P

[galaxy-dev] Creating multiple datasets in a libset

eritems(): wf_data['ds_map'][step_id] = {'src':'ld', 'id' :ds['id']} res = submit( api_key, api_url + 'workflows', wf_data, return_formatted=False) Rob Leclerc, PhD <http://www.linkedi

Re: [galaxy-dev] Creating multiple datasets in a libset

vcf /n /home/me/file3.vcf" I assume I should also increase the time.sleep() to reflect the uploading of extra files? Cheers, Rob Rob Leclerc, PhD <http://www.linkedin.com/in/robleclerc> <https://twitter.com/#!/robleclerc> P: (US) +1-(917)-873-3037 P: (Shanghai) +86-1-(861)-6

Re: [galaxy-dev] Creating multiple datasets in a libset

ted=False) if result_ds["state"] == 'ok': break else: time.sleep(1) Rob Leclerc, PhD <http://www.linkedin.com/in/robleclerc> <https://twitter.com/#!/robleclerc> P: (US) +1-(917)-873-3037 P: (Shanghai) +86-1-(861)-612-54

Re: [galaxy-dev] Creating multiple datasets in a libset

only solution that I can see that when the file_size != 0, you then ensure it that the file_size has not changed after a a short delay. Cheers, Rob Rob Leclerc, PhD <http://www.linkedin.com/in/robleclerc> <https://twitter.com/#!/robleclerc> P: (US) +1-(917)-873-3037 P: (Shanghai) +86

[galaxy-dev] Cloudman / galaxyIndicies

just need to rename specified filesystem in pd.yaml to ourGalaxyIndicies and then mount our CMs to /mnt/ourGalaxyIndicies/, or are their other locations I need to modify as well? Are the size and snap_id required? Cheers! Rob Rob Leclerc, PhD <http://www.linkedin.com/in/robleclerc> <https

Re: [galaxy-dev] Creating multiple datasets in a libset

;file_size'] != 0 and uploaded_file['file_size'] == last_filesize: break else: last_filesize = uploaded_file['file_size'] time.sleep(2) self.libset = libset return libset Rob Leclerc, P

[galaxy-dev] Running additional services

We're running cloudman and I would like to run a couple of additional services alongside galaxy. Is there a elegant way/place to add/run these services to existing galaxy code/scripts? Cheers, Rob Rob Leclerc, PhD <http://www.linkedin.com/in/robleclerc> <https://twitter.com/#!