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Question: How to update htseq-count?
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gravatar for faraz
4 months ago by
faraz • 0
faraz • 0 wrote:

I have recently inherited a galaxy installation from someone on a leave of absence . The former admin gave me a brief overview of it all.

A user has requested we update htseq-count. I see it is installed in /usr/local/bin . Do I just source the galaxy environment then do a pip update htseq-count ?
admin tool-install galaxy tool-update • 227 views
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modified 4 months ago by Jennifer Hillman Jackson ♦ 25k • written 4 months ago by faraz • 0
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gravatar for Jennifer Hillman Jackson
4 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Use the functions under the Admin masthead tab to manage tool installs/updates, dependencies, and other server operations. Admin >> Tool Management >> Manage tools should note if the tool has an available update in the ToolShed with an action to do the update.

Galaxy ecosystem:

Galaxy administrative resources and training:

If something goes wrong that you cannot solve (the server may have some advanced configurations to consider), you can ask the developers directly for troubleshooting help at Gitter: https://gitter.im/galaxyproject/Lobby or at the galaxy-dev mailing list https://galaxyproject.org/mailing-lists/.

Thanks! Jen, Galaxy team
ADD COMMENT • link written 4 months ago by Jennifer Hillman Jackson ♦ 25k

Thanks, I was able to make myself an admin and get access to the Tools update page in Galaxy. The new problem I face is the server has no internet access. So installing it from Galaxy fails when it tries to download htseq-count.

I was able to download the tar ball file of it: htseq_count-7f5a8d427b39.tar.gz . However, I am not sure how to "manually" install this? Is it possible from the admin interface?

ADD REPLY • link written 3 months ago by faraz • 0
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