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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___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
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