Question: Galaxy database piping and gzip format with copmression/decompression on the fly for .dat files
1
gravatar for pon.petr
3.9 years ago by
pon.petr10
United States
pon.petr10 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 • 1.0k views
ADD COMMENTlink modified 3.9 years ago by Martin Čech ♦♦ 4.7k • written 3.9 years ago by pon.petr10
2
gravatar for Martin Čech
3.9 years ago by
Martin Čech ♦♦ 4.7k
United States
Martin Čech ♦♦ 4.7k wrote:

Both piping and decompression on the fly are amongst the priorities however not implemented yet.

ADD COMMENTlink written 3.9 years ago by Martin Čech ♦♦ 4.7k

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

ADD REPLYlink written 3.9 years ago by pon.petr10

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 REPLYlink modified 3.9 years ago • written 3.9 years ago by Martin Čech ♦♦ 4.7k
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