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Question: Galaxy tar.gz upload and download
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gravatar for jasperkoehorst
3.7 years ago by
jasperkoehorst • 10
Netherlands
jasperkoehorst • 10 wrote:

When uploading a tar.gz file I noticed a file difference and this was explainable by the fact that it turned tar.gz. into a tar file. When downloading this tar file from galaxy I noticed after extraction that half of my files were gone.....

How to reproduce this?

Upload a tar.gz file, and save it to your computer
Extract the file and compare it to the content of the original file unpacked file, at least I noticed a major difference and many files were missing.

Anyone else on this?

 
tar.gz • 2.3k views
ADD COMMENT • link •
modified 3.7 years ago • written 3.7 years ago by jasperkoehorst • 10
1
gravatar for Daniel Blankenberg
3.7 years ago by
Daniel Blankenberg ♦♦ 1.7k
United States
Daniel Blankenberg ♦♦ 1.7k wrote:

Galaxy does not fully support the upload of .tar.gz files. Galaxy does support uploading single .gz files, eg. genes.bed.gz, which would be decompressed to genes.bed.

With the tar.gz upload, what is happening is the genes.bed.tar.gz is being decompressed to a single genes.bed.tar file in your history. When you download this dataset, you should get the whole tar as a single file that can contain one or more entries (you should be able to untar it).
ADD COMMENT • link written 3.7 years ago by Daniel Blankenberg ♦♦ 1.7k

that is the shock, after uploading and untarring by galaxy, when downloading that exact same history file the content is less, some folders and files from the tar are missing… This baffles me a lot as I am unsure why this could happen.

ADD REPLY • link modified 3.7 years ago • written 3.7 years ago by jasperkoehorst • 10

And also I prefer that galaxy is not unzipping or touching the files at all unless I tell them to, or tell them not to..

ADD REPLY • link written 3.7 years ago by jasperkoehorst • 10
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