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
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"
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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