Hi Birgit, Did you upload the same tarball you sent me previously, or was it a different tarball. If different, can you send it to me?
Thanks On Jun 18, 2012, at 8:18 PM, Birgit Crain wrote: > Hi Greg > > I just created a repository on the main toolshed and upload a tar ball. I got > the same error messages again as described in the email thread below. > > Regards > > Birgit Crain, Ph.D. | Sr. Professional Services Scientist | Complete > Genomics, Inc. > (650) 428-6023 office | (408) 605-3938 mobile > bcr...@completegenomics.com > > > From: Greg Von Kuster <g...@bx.psu.edu> > Date: Thursday, June 14, 2012 11:44 AM > To: Birgit Crain <bcr...@completegenomics.com> > Cc: "galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edu> > Subject: Re: [galaxy-dev] tool_data_table_config.xml.sample > > Hello Birgit, > > This issue has been resolved in changeset 7272:b761471d7590, which is > currently available from our Galaxy central repository. Both the Galaxy test > and Galaxy main tool sheds are running this latest changeset revision. > > Thanks very much for reporting this problem! > > Greg Von Kuster > > > On Jun 14, 2012, at 12:45 PM, Birgit Crain wrote: > >> Hi Greg >> I was using the Galaxy test toolshed to upload the files into a repository. >> On my Mac where I develop the tools I have a local instance that I loaded >> from zipped file (downloaded April galaxy-galaxy-dist-40f1816d6857.zip) >> running python 2.7. >> When I download the repository to a local instance on our server the tools >> and .loc file install fine (except that I don't have my datatypes defined >> right, working on that). >> >> Birgit Crain, Ph.D. | Sr. Professional Services Scientist | Complete >> Genomics, Inc. >> (650) 428-6023 office | (408) 605-3938 mobile >> bcr...@completegenomics.com >> >> >> From: Greg Von Kuster <g...@bx.psu.edu> >> Date: Wednesday, June 13, 2012 6:05 PM >> To: Birgit Crain <bcr...@completegenomics.com> >> Cc: "galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edu> >> Subject: Re: [galaxy-dev] tool_data_table_config.xml.sample >> >> Hi Birgit, >> >> What version of Galaxy are you running? You can determine this by typing >> "hg heads" in your Galaxy installation directory. Also, what version of >> Python are you running, and what database are you using? Can you also >> provide the complete paster log from you tool shed? >> >> Thanks, >> >> Greg Von Kuster >> >> On Jun 13, 2012, at 6:13 PM, Birgit Crain wrote: >> >>> Hi Greg >>> >>> Thanks for the tip. The .file items appear when I tar the directory on my >>> Mac, so I work around that issue and tar the directory on a UNIX server. >>> Thus said I happily did the same with another directory that contains tools >>> that are all dependent on the tool_data_table_conf.xml.sample and the >>> tool-data/cg_crr_files.loc.sample file. >>> >>> This directory has the following files: >>> >>> cgatools/README.txt >>> cgatools/tool_data_table_conf.xml.sample >>> cgatools/datatypes_conf.xml >>> cgatools/lib/galaxy/datatypes/completegenomics.py >>> cgatools/tool-data/cg_crr_files.loc.sample >>> cgatools/tools/cg_cgatools/listvariants.xml >>> cgatools/tools/cg_cgatools/junctiondiff.xml >>> cgatools/tools/cg_cgatools/snpdiff.xml >>> cgatools/tools/cg_cgatools/calldiff.xml >>> cgatools/tools/cg_cgatools/testvariants.xml >>> cgatools/tools/cg_cgatools/varfilter.xml >>> cgatools/tools/cg_cgatools/listtestvariants.xml >>> cgatools/tools/cg_cgatools/join.xml >>> cgatools/tools/cg_cgatools/varfilter_wrapper.pl >>> >>> When I upload this tar ball to the repository, one tool, calldiff, which is >>> alphabetically the first one in the list, loads properly and for the others >>> I get the following error message: >>> >>> Metadata was defined for some items in revision 'e183f52194a5'. Correct the >>> following problems if necessary and reset metadata. >>> join.xml - This file refers to a missing file cg_crr_files.loc. Upload a >>> file named cg_crr_files.loc.sample to the repository to correct this error. >>> junctiondiff.xml - This file refers to a missing file cg_crr_files.loc. >>> Upload a file named cg_crr_files.loc.sample to the repository to correct >>> this error. >>> listtestvariants.xml - This file refers to a missing file cg_crr_files.loc. >>> Upload a file named cg_crr_files.loc.sample to the repository to correct >>> this error. >>> listvariants.xml - This file refers to a missing file cg_crr_files.loc. >>> Upload a file named cg_crr_files.loc.sample to the repository to correct >>> this error. >>> snpdiff.xml - This file refers to a missing file cg_crr_files.loc. Upload a >>> file named cg_crr_files.loc.sample to the repository to correct this error. >>> testvariants.xml - This file refers to a missing file cg_crr_files.loc. >>> Upload a file named cg_crr_files.loc.sample to the repository to correct >>> this error. >>> varfilter.xml - This file refers to a missing file cg_crr_files.loc. Upload >>> a file named cg_crr_files.loc.sample to the repository to correct this >>> error. >>> >>> For the invalid tools is show this explanation: >>> >>> [Errno 2] No such file or directory: >>> '/var/opt/galaxy/g2cmnty/tmp/work_tmp/cg_crr_files.loc' >>> >>> >>> But I know the file is there …. Any suggestions? - I attached the tar ball >>> for a closer look. >>> Thanks >>> >>> >>> Birgit Crain, Ph.D. | Sr. Professional Services Scientist | Complete >>> Genomics, Inc. >>> (650) 428-6023 office | (408) 605-3938 mobile >>> bcr...@completegenomics.com >>> >>> >>> From: Greg Von Kuster <g...@bx.psu.edu> >>> Date: Wednesday, June 13, 2012 6:09 AM >>> To: Birgit Crain <bcr...@completegenomics.com> >>> Cc: "galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edu> >>> Subject: Re: [galaxy-dev] tool_data_table_config.xml.sample >>> >>> Hello Birgit, >>> >>> Your archive included several "._" scripts for some reason. None of these >>> were valid xml files, but since they have a .xml extension, the tool shed >>> attempts to parse them which results in the error message you got: >>> >>> not well-formed (invalid token): line 1, column 0 >>> >>> Here is the contents of your achive: >>> >>> -rw-r--r-- 1 gvk wheel 6148 Jun 6 16:09 .DS_Store >>> -rw-r--r-- 1 gvk wheel 171 May 25 13:44 >>> ._Calculate_TestVariants_Variant_Frequencies.xml >>> -rwxr-xr-x 1 gvk wheel 171 May 3 19:19 >>> ._Calculate_TestVariants_Variant_Frequencies_0_1_0.pl >>> -rw-r--r-- 1 gvk wheel 171 May 31 13:39 ._List_Unique_Variants.xml >>> -rwxr-xr-x 1 gvk wheel 171 May 3 12:50 >>> ._List_Unique_Variants_2_1_0.pl >>> -rw-r--r-- 1 gvk wheel 1950 May 25 13:44 >>> Calculate_TestVariants_Variant_Frequencies.xml >>> -rwxr-xr-x 1 gvk wheel 9242 May 3 19:19 >>> Calculate_TestVariants_Variant_Frequencies_0_1_0.pl >>> -rw-r--r-- 1 gvk wheel 13625 May 31 13:39 List_Unique_Variants.xml >>> -rwxr-xr-x 1 gvk wheel 22321 May 3 12:50 List_Unique_Variants_2_1_0.pl >>> >>> I eliminated all of the "._" files and created a new archive which uploaded >>> successfully. I've attached the archive. >>> >>> >>> Greg Von Kuster >>> >>> >>> On Jun 12, 2012, at 4:38 PM, Birgit Crain wrote: >>> >>>> Thanks, Greg >>>> >>>> I tried uploading the same tar ball without the >>>> tool_data_table_config.xml.sample file and the tools load fine (to >>>> troubleshoot I added only tools that actually do not depend on the file). >>>> As soon as I add the .sample file to the tar ball I get the error message. >>>> >>>> Thanks, Birgit >>>> >>>> From: Greg Von Kuster <g...@bx.psu.edu> >>>> Date: Tuesday, June 12, 2012 1:18 PM >>>> To: Birgit Crain <bcr...@completegenomics.com> >>>> Cc: "galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edu> >>>> Subject: Re: [galaxy-dev] tool_data_table_config.xml.sample >>>> >>>> Hi Birgit, >>>> >>>> I don't see any problem with your xml definition below. Are you sure the >>>> problem is not with another file in the tarball? If you can send me the >>>> tarball, I'll take a look. >>>> >>>> Greg Von Kuster >>>> >>>> >>>> On Jun 12, 2012, at 4:09 PM, Birgit Crain wrote: >>>> >>>>> Hi >>>>> >>>>> I'm developing tools that use an entry in the tool_data_table_config.xml >>>>> file. For upload into a repository I created a >>>>> tool_data_table_config.xml.sample file with the corresponding table >>>>> entry. The structure for the file I copied from the >>>>> tool_data_table_config.xml. in the galaxy download. >>>>> >>>>> <tables> >>>>> <!-- Start location of cgatools crr files --> >>>>> <table name="cg_crr_files" comment_char="#"> >>>>> <columns>value, dbkey, name, path</columns> >>>>> <file path="tool-data/cg_crr_files.loc" /> >>>>> </table> >>>>> <!-- End Location of cgatools crr files --> >>>>> </tables> >>>>> >>>>> When I upload the tar ball into the repository the tools won't load >>>>> properly and I get the following message: >>>>> >>>>> not well-formed (invalid token): line 1, column 0 >>>>> >>>>> Any suggestions what I'm missing or how to fix this error? >>>>> >>>>> Thanks, Birgit >>>>> >>>>> >>>>> >>>>> The contents of this e-mail and any attachments are confidential and only >>>>> for use by the intended recipient. Any unauthorized use, distribution or >>>>> copying of this message is strictly prohibited. If you are not the >>>>> intended recipient please inform the sender immediately by reply e-mail >>>>> and delete this message from your system. Thank you for your co-operation. >>>>> ___________________________________________________________ >>>>> Please keep all replies on the list by using "reply all" >>>>> in your mail client. To manage your subscriptions to this >>>>> and other Galaxy lists, please use the interface at: >>>>> >>>>> http://lists.bx.psu.edu/ >>>> >>>> >>>> >>>> The contents of this e-mail and any attachments are confidential and only >>>> for use by the intended recipient. Any unauthorized use, distribution or >>>> copying of this message is strictly prohibited. If you are not the >>>> intended recipient please inform the sender immediately by reply e-mail >>>> and delete this message from your system. Thank you for your co-operation. >>>> <scripts.tar.gz>___________________________________________________________ >>>> Please keep all replies on the list by using "reply all" >>>> in your mail client. To manage your subscriptions to this >>>> and other Galaxy lists, please use the interface at: >>>> >>>> http://lists.bx.psu.edu/ >>> >>> >>> >>> The contents of this e-mail and any attachments are confidential and only >>> for use by the intended recipient. Any unauthorized use, distribution or >>> copying of this message is strictly prohibited. If you are not the intended >>> recipient please inform the sender immediately by reply e-mail and delete >>> this message from your system. Thank you for your co-operation. >>> <cgatools.tar.gz> >> >> >> >> The contents of this e-mail and any attachments are confidential and only >> for use by the intended recipient. Any unauthorized use, distribution or >> copying of this message is strictly prohibited. If you are not the intended >> recipient please inform the sender immediately by reply e-mail and delete >> this message from your system. Thank you for your co-operation. > > > > The contents of this e-mail and any attachments are confidential and only for > use by the intended recipient. Any unauthorized use, distribution or copying > of this message is strictly prohibited. If you are not the intended recipient > please inform the sender immediately by reply e-mail and delete this message > from your system. Thank you for your co-operation.
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