User: pstew
pstew • 40
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Posts by pstew
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C: Galaxy API file upload times out
... Thanks for writing. No proxy. It's being used as a standalone script for testing prior to being incorporated into a Galaxy tool. A friend from our institution tried the script outside of our institution's network and it works fine. We've also tried uploading different files and they work just fine.T ...
written 14 months ago by
pstew • 40
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... We have a Python script that uses the Galaxy API to upload files to a user's most recently used history on one of our institution's Galaxy instances. It has been working mostly fine for uploading from machines on our institution's network (it timed out on us one time), but it times out for our colla ...
written 14 months ago by
pstew • 40
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... Our building's internet was having issues. IT replaced some switches, and I've since moved to a wired connection instead of wireless. It built and ran just fine after this. Try following these instructions: https://wiki.galaxyproject.org/Admin/Config/Eggs .
...
written 3.3 years ago by
pstew • 40
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... EDIT: Copying the egg to /eggs worked like a charm. Galaxy runs now. Hurray! Thanks for your help and patience.
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Do I just need to download the json.egg and put it in the /eggs directory, or do I need to download it and scramble it to install it? Trying to get ...
written 3.7 years ago by
pstew • 40
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... After numerous attempts, it looks like I'm down to simplejson failing a fetch from
python ./scripts/fetch_eggs.py
I then tried taking your advice (following the instructions for If your Galaxy server does not have Internet access ) using a different machine with a working version of Galaxy, but ...
written 3.7 years ago by
pstew • 40
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... Great, thank you! Hopefully I can use this as a temporary fix. Our IT people are looking into the machine's connectivity issues (there have been intermittent problems in the building).
...
written 3.7 years ago by
pstew • 40
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... Thanks, this is what I figured. As I mentioned above, I can keep rerunning python ./scripts/fetch_eggs.py and get a few extra eggs each time, but eventually it will timeout and error on me. I've been running this manually all day. Is there an easy way to manually download all of these at once using ...
written 3.7 years ago by
pstew • 40
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... It looks like it's a connection issue. I can keep rerunning python ./scripts/fetch_eggs.py and get a few extra eggs each time, but eventually it will timeout and error on me. I've been running this manually all day. Is there an easy way to manually download all of these at once using wget or other ...
written 3.7 years ago by
pstew • 40
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... I deleted all eggs in ./eggs/, ran python ./scripts/fetch_eggs.py and got the following:
Traceback (most recent call last):
File "./scripts/fetch_eggs.py", line 46, in <module>
c.resolve() # Only fetch eggs required by the config
File "/home/stewarpa/galaxy-dist/lib/galaxy/eggs/__init ...
written 3.7 years ago by
pstew • 40
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... I'd say I'm an intermediate Linux user. I'm trying to get Galaxy setup on a new install of CentOS. Python 2.7 is installed. Following the instructions at https://wiki.galaxyproject.org/Admin/GetGalaxy .Things start initializing just fine when I run sh run.sh, but then I hit this error:
<snip> ...
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