Unable to upload files to local Galaxy server

Question: Unable to upload files to local Galaxy server

3.6 years ago by

United States

Hello,

I am trying to upload a small .txt file to my local instance of galaxy (I am running on top of CentOS 6.5) using the Upload File tool. However, the upload job fails, and I get the following error:

/home/vazimi/Downloads/galaxy-release_15.05/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/pysam/__init__.py:1: RuntimeWarning: __builtin__.file size changed, may indicate binary incompatibility
  from csamtools import *
/home/vazimi/Downloads/galaxy-release_15.05/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/pysam/__init__.py:1: RuntimeWarning: __builtin__.file size changed, may indicate binary incompatibility
  from csamtools import *

Any ideas?

Thanks,

Vahid

upload galaxy • 1.1k views

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modified 3.6 years ago by Daniel Blankenberg ♦♦ 1.7k • written 3.6 years ago by vahid.azimi.p3 • 10

3.6 years ago by

Daniel Blankenberg ♦♦ 1.7k

United States

Daniel Blankenberg ♦♦ 1.7k wrote:

Hi Vahid,

One important thing here is that the Galaxy 'maf' datatype refers to the "Multiple Alignment Format" (https://genome.ucsc.edu/FAQ/FAQformat.html#format5), while it looks like you are dealing with a file that is "Mutation Annotation Format" (https://wiki.nci.nih.gov/display/TCGA/Mutation+Annotation+Format+%28MAF%29+Specification).

However, the error that you are seeing is due to a bug in the pysam egg that we distribute with Galaxy, that we should have fixed within the next release.

ADD COMMENT • link written 3.6 years ago by Daniel Blankenberg ♦♦ 1.7k

Daniel,

Ah, thank you for the clarification. In that case I suppose I have to wait for the next release.

Thanks for all the great work you guys do!

-Vahid

ADD REPLY • link written 3.6 years ago by vahid.azimi.p3 • 10

3.6 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

It appears that the file uploaded is not detected as plain text format. Please double check the format.

If necessary, it is possible to set the "datatype" upon upload. Although it is important note that this will not transform the file type if it is not in plain text.

Hopefully this will resolve the issue, but let us know if it does not. You can share a snippet of the file if needed (via a github "gist" link, etc). Thanks, Jen, Galaxy team

ADD COMMENT • link written 3.6 years ago by Jennifer Hillman Jackson ♦ 25k

Hi Jen,

Thank you for the reply. The file is a MAF file, but is saved as a txt file. I've tried to load it while setting the datatype as txt, maf, as well as auto-detect, but still no luck. I have shared a snippet of the file below.

Thanks,

Vahid

ADD REPLY • link modified 3.6 years ago • written 3.6 years ago by vahid.azimi.p3 • 10

Hi -for the gist, right-click on the title to capture the link, then send that pls. I may just be me, but I don't know how to access that way (YET!) as just a quick browser view mode.

Double check that no info specific to your instance is in there when posting up here. Just XXX it out as needed. Paths are OK to leave in.

Thanks - we'll sort it out! Jen

PS: I am going to guess a bit here (sometimes I get it right!). Maybe try this first... IF it is MAF format, then you could just load as MAF. The upload tool does some format validation and if the format is set as "text" instead of autodetect, this can sometimes trigger an unknown file type, and that defaults to an interpretation as an unknown binary format, which looks an awful lot like what you first reported. The once loaded you can use text manipulation tools/edit attributes to slice & dice into tab format and perform the next steps you have planned.

This behaviour is something we are tracking and have plans to smooth out to make usage easier - but automated tools can only do so much.

ADD REPLY • link written 3.6 years ago by Jennifer Hillman Jackson ♦ 25k

Hi Jen,

Thanks for your reply. The files I'm working with are downloaded as .txt files but are in MAF format...I have tried uploading them while setting the datatype as txt files, I have tried setting datatype MAF format, as well as auto-detect. I have also tried saving the txt files as .maf and uploading them as datatype MAF files, but still no luck.

I truly appreciate your time and help on this matter.

-Vahid

ADD REPLY • link written 3.6 years ago by vahid.azimi.p3 • 10

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