local galaxy - how to unzip files

Hello everyone,

So we have installed a local galaxy and most tools we use work perfectly fine. However, a tool I use for subsampling creates a gzipped file as output in the local galaxy. In the online galaxy a unzipped file is created.

Is there a possibility to unzip files on the local galaxy as the other tools in the workflow cannot deal with a zipped file? The online galaxy however seems to not have any issues.

Does anybody know how to resolve this issue?

Thank you very much for your time!

can you link the tool please?

Generally Galaxy supports compressed files, and if a tool requires uncompressed input Galaxy will decompress it on the fly and then supply to the tool. There is a bit of configuration involved so you can decide what formats you support compressed and which should always be decompressed.

fastqsanger will stay compressed in gz/bz2 unless you specifically set the datatype to an uncompressed one when creating/uploading. See auto_compressed_types config flag:

Thank you for your reply.

The tool is called: seqtk_sample. The issue is that it just creates the zipped files on the local galaxy but not on the online galaxy. If I use the same tool on the online galaxy, the file is not compressed.

As I said, this is configurable and means that your local configuration (or Galaxy version) differs. What Galaxy version are you using?

this tool support .gz compression (not bz2), and the format of the output is the same as format of the input. So example.fastqsanger.gz will result in output.fastqsanger.gz.