tgz file uploading and supporting

4.5 years ago by

fubar ♦ 1.1k

Australia

fubar ♦ 1.1k wrote:

Simple compressed files such as the fastq.gz archive also in that directory @

http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm10847NfkbTnfaIggrabRawDataRep5.fastq.gz

will upload and automatically uncompress - I just tested that one - it contains a single fastq which Galaxy can handle as expected.

Tarball archives (.tgz) like the one you report cannot be handled (at present!) where they contain multiple files (in this case there are two files, one called "[...]reject.fastq"). The new dataset collections being added to Galaxy may allow this to be fixed in future but for now, one possible but ugly way around this is to grab the .tgz file, uncompress it and upload the bits you want separately - sorry this is not convenient but it will at least work so you can get on with your research?

ADD COMMENT • link modified 4.5 years ago • written 4.5 years ago by fubar ♦ 1.1k

Can we develop a toolshed to make tgz supported in public galaxy(e.g. usegalaxy.org) by ourselves?

ADD REPLY • link written 4.5 years ago by luyizhen • 10

You can create a tool that downloads a tarball extracts its content and creates X outout files. But that is rather hackish and I do not think that will be included on usegalaxy.org. Work is underway to support such features in the near future.

ADD REPLY • link written 4.5 years ago by Bjoern Gruening ♦ 5.1k

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