Re: [galaxy-dev] Problem with GMAP datatypes
I'll give it a try and let you know if I run into any more problemsThanksThonOn Feb 10, 2012, at 12:00 PM, Greg Von Kuster wrote: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 :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 :10: (WARNING/2) Explicit markup ends without a blank line; unexpected unindent. >> >> docutils WARNING 2012-02-09 12:51:47,332 :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 :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.
Re: [galaxy-dev] Problem with GMAP datatypes
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 :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 :10: (WARNING/2) Explicit >> markup ends without a blank line; unexpected unindent. >> >> docutils WARNING 2012-02-09 12:51:47,332 :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 :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/rep
Re: [galaxy-dev] Problem with GMAP datatypes
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 :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 :10: (WARNING/2) Explicit > markup ends without a blank line; unexpected unindent. > > docutils WARNING 2012-02-09 12:51:47,332 :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 :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
