Hello L-A,

Would you be able to help with a bit more detail and testing? #2 sounds like it may be the issue, but without knowing more right now, I'll provided the next troubleshooting steps.

1 - this is in your own install and it is current with the latest -dist or are you using -central (which pull?). Did something change between the last successful BAM load and the new problem?

2 - "without copying" them means maybe that you are using a symbolic link at your own site? This "load" is into a Library (this is how to move data transferred outside of the Galaxy mechanisms into a history, i.e. around a local file system by direct copy or similar). Load into a Library first, then copy to history. Instruction in wiki here:
http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files

3 - or do you mean "without copying" by using the FTP method set up locally, followed by a load into a history?

4 - BAM file metadata (pencil icon -> Edit options) looks OK? Or, this is the problem?

5 - SAMTools is loaded into your instance? Tools function on other BAM files or all? Some simple SAMTools commands (that work with BAM files) function line command OK on these (to rule out problem with BAM files themselves - missing .bai index could be a problem).

6 - if you start with the same data and convert SAM->BAM within Galaxy, does the SAM load and is the resulting BAM file OK?

7 - If you load the BAM file at the public Galaxy web site (using FTP), the load is successful and the BAM file once imported into a history appears OK? Please share link from this test in case we need to examine. (Options -> Share or Publish, generate link, email to me and I can share with dev team if needed).

Thanks for providing more info or perhaps you will find that one of these uncovers the issue,

Best,

Jen
Galaxy team

On 7/18/11 2:05 AM, Louise-Amélie Schmitt wrote:
Hello everyone

Whenever we try to load BAM files without copying them, we get an error
stating the files need grooming, and can't use them at all.

Is it this serious? Would there be a way to bypass that?

Thanks!
L-A
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