Thon,

I believe this is fixed in change set 6711:62fc9e053835, which is now available 
in out central repo.  However, I do not have access to any data of the required 
type, so if you still encounter problems, could you send me some data that I 
can use to reproduce the behavior?

Thanks!

Greg

On Feb 9, 2012, at 9:04 PM, Greg Von Kuster wrote:

> Hi Thon,
> 
> I've been working on fixes which I believe may be related to this.  When 
> uploading a file, the proprietary datatypes / sniffers (datatypes included in 
> installed tool shed repositories) are not correctly handled by the upload 
> process.  Also, when running jobs, if setting metadata externally, the same 
> issue occurs.  I'm very close to a fix for this - I just need to polish up 
> the changes.  I'm planning to have the fix committed tomorrow - I'll let you 
> know.
> 
> Thanks for reporting this.
> 
> Greg
> 
> 
> On Feb 9, 2012, at 5:32 PM, Anthonius deBoer wrote:
> 
>> I tried to install the GMAP from the main toolshed, but I am getting this 
>> error when I actually try to run the GSNAP/GMAP tools
>> 
>> It seems that there is a problem with the definition of the datatypes...When 
>> I check the paster.log it does complain a little, when loading GMAP stuff, 
>> but it seems just a problem with the markup of the help text
>> 
>> Any ideas?
>> 
>> 
>> Error in galaxy when running GSNAP
>> WARNING:galaxy.datatypes.registry:Error loading datatype with extension 
>> 'gmapdb': 'module' object has no attribute 'gmap'
>> WARNING:galaxy.datatypes.registry:Error loading datatype with extension 
>> 'gmapsnpindex': 'module' object has no attribute 'gmap'
>> WARNING:galaxy.datatypes.registry:Error loading datatype with extension 
>> 'iit': 'module' object has no attribute 'gmap'
>> WARNING:galaxy.datatypes.registry:Error loading datatype with extension 
>> 'splicesites.iit': 'module' object has no attribute 'gmap'
>> WARNING:galaxy.datatypes.registry:Error loading datatype with extension 
>> 'introns.iit': 'module' object has no attribute 'gmap'
>> WARNING:galaxy.datatypes.registry:Error loading datatype with extension 
>> 'snps.iit': 'module' object has no attribute 'gmap'
>> WARNING:galaxy.datatypes.registry:Error loading datatype with extension 
>> 'gmap_annotation': 'module' object has no attribute 'gmap'
>> WARNING:galaxy.datatypes.registry:Error loading datatype with extension 
>> 'gmap_splicesites': 'module' object has no attribute 'gmap'
>> WARNING:galaxy.datatypes.registry:Error loading datatype with extension 
>> 'gmap_introns': 'module' object has no attribute 'gmap'
>> WARNING:galaxy.datatypes.registry:Error loading datatype with extension 
>> 'gmap_snps': 'module' object has no attribute 'gmap'
>> WARNING:galaxy.datatypes.registry:Error appending sniffer for datatype 
>> 'galaxy.datatypes.gmap:IntervalAnnotation' to sniff_order: No module named 
>> gmap
>> WARNING:galaxy.datatypes.registry:Error appending sniffer for datatype 
>> 'galaxy.datatypes.gmap:SpliceSiteAnnotation' to sniff_order: No module named 
>> gmap
>> WARNING:galaxy.datatypes.registry:Error appending sniffer for datatype 
>> 'galaxy.datatypes.gmap:IntronAnnotation' to sniff_order: No module named gmap
>> WARNING:galaxy.datatypes.registry:Error appending sniffer for datatype 
>> 'galaxy.datatypes.gmap:SNPAnnotation' to sniff_order: No module named gmap
>> 
>> PASTER.LOG
>> ==========
>> 
>> galaxy.util.shed_util DEBUG 2012-02-09 12:51:43,862 Installing repository 
>> 'gmap'
>> galaxy.util.shed_util DEBUG 2012-02-09 12:51:43,914 Cloning 
>> http://toolshed.g2.bx.psu.edu/repos/jjohnson/gmap
>> galaxy.util.shed_util DEBUG 2012-02-09 12:51:46,834 Updating cloned 
>> repository to revision "93911bac43da"
>> docutils WARNING 2012-02-09 12:51:47,128 <string>:10: (WARNING/2) Explicit 
>> markup ends without a blank line; unexpected unindent.
>> 
>> galaxy.util.shed_util DEBUG 2012-02-09 12:51:47,190 Adding new row (or 
>> updating an existing row) for repository 'gmap' in the tool_shed_repository 
>> table.
>> docutils WARNING 2012-02-09 12:51:47,238 <string>:10: (WARNING/2) Explicit 
>> markup ends without a blank line; unexpected unindent.
>> 
>> docutils WARNING 2012-02-09 12:51:47,332 <string>:10: (WARNING/2) Explicit 
>> markup ends without a blank line; unexpected unindent.
>> 
>> galaxy.tools DEBUG 2012-02-09 12:51:47,391 Reloading section: GMAP
>> galaxy.tools DEBUG 2012-02-09 12:51:47,413 Loaded tool id: 
>> toolshed.g2.bx.psu.edu/repos/jjohnson/gmap/gmap_iit_store/2.0.0, version: 
>> 2.0.0.
>> docutils WARNING 2012-02-09 12:51:47,445 <string>:10: (WARNING/2) Explicit 
>> markup ends without a blank line; unexpected unindent.
>> 
>> galaxy.tools DEBUG 2012-02-09 12:51:47,462 Loaded tool id: 
>> toolshed.g2.bx.psu.edu/repos/jjohnson/gmap/gsnap/2.0.1, version: 2.0.1.
>> galaxy.tools DEBUG 2012-02-09 12:51:47,482 Loaded tool id: 
>> toolshed.g2.bx.psu.edu/repos/jjohnson/gmap/gmap_snpindex/2.0.0, version: 
>> 2.0.0.
>> galaxy.tools DEBUG 2012-02-09 12:51:47,501 Loaded tool id: 
>> toolshed.g2.bx.psu.edu/repos/jjohnson/gmap/gmap_build/2.0.0, version: 2.0.0.
>> galaxy.tools DEBUG 2012-02-09 12:51:47,534 Loaded tool id: 
>> toolshed.g2.bx.psu.edu/repos/jjohnson/gmap/gmap/2.0.1, version: 2.0.1.
>> galaxy.datatypes.registry DEBUG 2012-02-09 12:51:49,247 Loading datatypes 
>> from 
>> /mnt/ngs/analysis/tdeboer/galaxy-data/shed_tools/toolshed.g2.bx.psu.edu/repos/jjohnson/gmap/93911bac43da/gmap/tool-data/datatypes_conf.xml
>> galaxy.datatypes.registry DEBUG 2012-02-09 12:51:49,248 Loaded sniffer for 
>> datatype 'galaxy.datatypes.gmap:IntervalAnnotation'
>> galaxy.datatypes.registry DEBUG 2012-02-09 12:51:49,248 Loaded sniffer for 
>> datatype 'galaxy.datatypes.gmap:SpliceSiteAnnotation'
>> galaxy.datatypes.registry DEBUG 2012-02-09 12:51:49,248 Loaded sniffer for 
>> datatype 'galaxy.datatypes.gmap:IntronAnnotation'
>> galaxy.datatypes.registry DEBUG 2012-02-09 12:51:49,248 Loaded sniffer for 
>> datatype 'galaxy.datatypes.gmap:SNPAnnotation'
>> 172.17.50.220 - - [09/Feb/2012:12:51:43 -0700] "POST 
>> /admin_toolshed/install_repository?tool_shed_url=http%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F&repo_info_dict=5c18aa85fc57b4d2abf667fb4a49e9cb68d77ae9%3A7b22676d6170223a205b22474d41502047534e415020206d617070696e6720616e6420616c69676e6d656e7420222c2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f6a6a6f686e736f6e2f676d6170222c2022393339313162616334336461225d7d&includes_tools=True
>>  HTTP/1.1" 302 - 
>> "http://srp106:8080/admin_toolshed/install_repository?tool_shed_url=http://toolshed.g2.bx.psu.edu/&repo_info_dict=5c18aa85fc57b4d2abf667fb4a49e9cb68d77ae9:7b22676d6170223a205b22474d41502047534e415020206d617070696e6720616e6420616c69676e6d656e7420222c2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f6a6a6f686e736f6e2f676d6170222c2022393339313162616334336461225d7d&includes_tools=True";
>>  "Mozilla/5.0 (Windows NT 6.1; WOW64; rv:9.0.1) Gecko/20100101 Firefox/9.0.1"
>> 172.17.50.220 - - [09/Feb/2012:12:51:49 -0700] "GET 
>> /admin_toolshed/browse_repositories?status=done&message=Installed+1+repository+and+all+tools+were+loaded+into+tool+panel+section+%3Cb%3EGMAP%3C%2Fb%3E%3A%3Cbr%2F%3EInstalled+repositories%3A+gmap.%3Cbr%2F%3E
>>  HTTP/1.1" 200 - 
>> "http://srp106:8080/admin_toolshed/install_repository?tool_shed_url=http://toolshed.g2.bx.psu.edu/&repo_info_dict=5c18aa85fc57b4d2abf667fb4a49e9cb68d77ae9:7b22676d6170223a205b22474d41502047534e415020206d617070696e6720616e6420616c69676e6d656e7420222c2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f6a6a6f686e736f6e2f676d6170222c2022393339313162616334336461225d7d&includes_tools=True";
>>  "Mozilla/5.0 (Windows NT 6.1; WOW64; rv:9.0.1) Gecko/20100101 Firefox/9.0.1"
>> 
>> 
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