Uploading data to galaxy

Question: Uploading data to galaxy

21 months ago by

I am having an issue uploading files onto the galaxy server. It comes with an error, problem decompressing gzipped data. Can you help with this issue?

rna-seq • 618 views

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modified 21 months ago • written 21 months ago by stafford.vigors • 0

21 months ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Some reports of upload failures have come in. These are no longer reproducible and the root cause is not known. The first pass solution is to try it now, then troubleshoot if you are still having problems.

Troubleshooting:

When .gz compressed data fails to uncompress the issue is usually an incompatibility between the server resources used to uncompress data and the compression resources used to create the file. That or the file is over 2 GB and was browsed for upload instead of FTP being used.
If the failure is persistent even with FTP, then uncompress the data before loading into Galaxy. This also helps find problems - if the data will not uncompress locally, it will not uncompress in Galaxy, generally indicating that the file is not complete due to an earlier partial transfer upstream of Galaxy.

Help for upload:

https://new.galaxyproject.org/learn/galaxy-ngs101/#getting-data-in

Thanks! Jen, Galaxy team

ADD COMMENT • link written 21 months ago by Jennifer Hillman Jackson ♦ 25k

Hi,

Has the "leave .gz files compressed" function/policy been disabled? I have just uploaded a batch of gzip files and they were automatically decompressed to my surprise.

Bao

ADD REPLY • link written 21 months ago by Bao Ho • 80

Assign the datatype fastq.gz or fastqsanger.gz to the file in the upload tool. This will preserve the compressed format.

If datatype autodetect (default) is used then the file will uncompress.

ADD REPLY • link written 21 months ago by Jennifer Hillman Jackson ♦ 25k

21 months ago by

stafford.vigors • 0

stafford.vigors • 0 wrote:

Hi thank you for your advice, I tried some of the advice and it seems that my files may be too big to upload, I have also tried uploading using filezilla ans also importing directly from NGS provider. When I try to import directly from the provider site I get this message ,urlopen error ftp error: 503 Login with USER first' I think if I can get this working this may be the best option, any advice?

ADD COMMENT • link written 21 months ago by stafford.vigors • 0

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