Bump. Anyone got ideas regarding the issue below, please? ATM we're not able to use Galaxy as we would like. Thanks, Chris On 05/01/10 11:18, Chris Cole wrote:
Hi Kelly,
Just getting back to this following the holidays.
On 22/12/09 21:32, Kelly Vincent wrote:
Hi Chris,
Can you confirm that you have a recent changeset (today we're at 3192:828d9f9dcb29)?
'hg tip' returns 3137:ddd9d5ac0457
If you're using an earlier version, either update or check that <Galaxy root>/lib/galaxy/datatypes/registry.py contains the following line: 'sam' : 'text/plain', (it should be line 164, as part of the self.mimetypes_by_extension dictionary definition).
Yup, it's there
In either case, make sure the line: <datatype extension="sam" type="galaxy.datatypes.tabular:Sam" display_in_upload="true"/> appears in <Galaxy root>/datatypes_conf.xml. It should be around line 51, inside the tag: <registration converters_path="lib/galaxy/datatypes/converters">
Nope. Not in there.
I've added it and it works for small files, but not large ones. Small is 119 lines and large 20 million lines. There are no errors in paster.log, now. Galaxy simply falls over.
Would an update solve it? Thanks for your help,
Chris
Let us know what you find.
Regards, Kelly
On Dec 18, 2009, at 11:35 AM, Chris Cole wrote:
Hi,
On our local install, we've just enabled bowtie NGS mapping and although the search runs fine and the output is viewable in Galaxy, any attempt to save it brings down the server.
The only error in paster.log is: galaxy.datatypes.registry WARNING 2009-12-18 16:32:38,517 unknown mimetype in data factory sam
Tried it on large files and small files with the same effect.
Trying save as fails with an 'unable to read file error'. Anyone have any ideas? Cheers,
Chris
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