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Question: Galaxy database piping and gzip format with copmression/decompression on the fly for .dat files
1
gravatar for pon.petr
4.3 years ago by
pon.petr • 10
United States
pon.petr • 10 wrote:

Hello,

We are running out of space on our Galaxy server. Is there a way for tools in a workflow (or in history) to avoid storing data in intermediate steps (as piping in unix)? Is there a way to store .dat files in the database in compressed format (ie gzip) with compression/decompression on the fly, when galaxy tool writes/asks for .dat file? 

If it is not available in galaxy yet, we would be happy to code this things and share with everybody.

Thank you.

Petr.

 
galaxy database • 1.1k views
ADD COMMENT • link •
modified 4.3 years ago by Martin Čech ♦♦ 4.9k • written 4.3 years ago by pon.petr • 10
2
gravatar for Martin Čech
4.3 years ago by
Martin Čech ♦♦ 4.9k
United States
Martin Čech ♦♦ 4.9k wrote:

Both piping and decompression on the fly are amongst the priorities however not implemented yet.
ADD COMMENT • link written 4.3 years ago by Martin Čech ♦♦ 4.9k

How I can help you to develop piping and compression/decompression on the fly? Thank you

ADD REPLY • link written 4.3 years ago by pon.petr • 10

If you want to code you can fork this repo: https://bitbucket.org/galaxy/galaxy-central and eventually create a pull request once you implement and test the functionality.

Also see the Develop hub page: https://wiki.galaxyproject.org/Develop

If you want to discuss this join us at irc channel #galaxyproject at freenode

ADD REPLY • link modified 4.3 years ago • written 4.3 years ago by Martin Čech ♦♦ 4.9k
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