Question: Adding tools from the command-line to Galaxy Standalone on Jetstream
0
gravatar for matt.chambers42
19 months ago by
matt.chambers4250 wrote:

I have created an instance of Galaxy on Jetstream and I have root SSH access. But when I run the install-repository script, like: install-repository "--url http://toolshed.g2.bx.psu.edu/ -o devteam --name data_manager_sam_fasta_index_builder"

I first got an error about not finding [server:main]. I fixed that by changing the process name in /etc/supervisor/conf.d/galaxy.conf and galaxy.ini (so now it's main instead of web0). But now I'm getting an error that doesn't suggest a way to fix it:

Processing:      --url http://toolshed.g2.bx.psu.edu/ -o devteam --name data_manager_sam_fasta_index_builder
HTTP Error 500: Internal Server Error

<html>
<head>
<style type="text/css">
body { color: #303030; background: #dfe5f9; font-family:"Lucida Grande",verdana,arial,helvetica,sans-serif; font-size:12px; line-height:16px; }
.content { max-width: 720px; margin: auto; margin-top: 50px; }
</style>
Internal Server Error

</head>
<body>

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.

</body> </html>
admin jetstream galaxy • 565 views
ADD COMMENTlink modified 19 months ago • written 19 months ago by matt.chambers4250

Please check your Galaxy's log. I am unsure about the jetstream image details but it should be storing the log of Galaxy process somewhere.

ADD REPLYlink written 19 months ago by Martin Čech ♦♦ 4.7k

It seems the install-repository script is not intended (?) to work with the Jetstream instance. Instead, it points to using an ansible playbook: https://github.com/afgane/galaxy-tools-playbook

ADD REPLYlink written 19 months ago by matt.chambers4250
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