It is highly recommended that you get the latest source from our Galaxy 
distribution repository using mercurial.  As Peter stated, this will enable you 
to get regular updates as new Galaxy distribution releases occur.  Your 
downloaded zip file contains what we consider a very old release.  The Galaxy 
distribution is available using mercurial at this url.

https://bitbucket.org/galaxy/galaxy-dist

The changes I made to the Galaxy datatypes components were implemented to 
provide support for proprietary datatypes contained in installed tool shed 
repositories, so are not related to problems that may occur when uploading.

If I understand the issue correctly, it sounds like there is a problem when you 
upload your file with contents that are a custom datatype which you've 
subclassed from the Galaxy binary datatype.  If your file is being changed by 
the Galaxy sniff process, then there may be a bug in that process.  What do 
your paster logs show?

Also, your data attachments have been lost in the mail thread - did only Peter 
get them?

Greg Von Kuster

On Feb 25, 2012, at 5:20 AM, Peter Cock wrote:

> On Sat, Feb 25, 2012 at 9:40 AM, Yingwei HU <husi...@gmail.com> wrote:
>> Dear Peter,
>> 
>> I am sorry I do not know the version of my galaxy by using hg. I directly
>> downloaded the zip file from the address:
>> http://dist.g2.bx.psu.edu/galaxy-dist.tip.zip
> 
> That would be fine for a one-off test installation, but it will make
> doing an upgrade extremely difficult. That is why the Galaxy
> recommend using the mercurial (hg) source code system.
> 
>> The zipped files are compressed on 2011-06-29. Is this version too old?
>> 
> 
> The changes I am thinking of were earlier this month (Feb 2012)
> by Greg on galaxy-central and have not yet been released on
> galaxy-dist. Hopefully he can provide more information next week.
> 
> e.g. https://bitbucket.org/galaxy/galaxy-central/changeset/865d998a693d
> 
> Regards,
> 
> Peter
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