Hello Birgit, I've committed a fix for this is change set 7302:c4f325ba7caa, which is available in the Galaxy central repository, and is running on both Galaxy tool sheds. I've made sure that your cg_cgatools_linux repository is now functional.
Thanks very much for finding this additional issue, and for your patience in resolving these problems. Hopefully things will be smoother from here on for you, but please let me know if you do encounter additional problems. There are many complexities in making the various tools work as expected in the tool shed, so issues like this tend to crop up every so often. Thanks again, Greg Von Kuster On Jun 20, 2012, at 11:41 AM, Birgit Crain wrote: > I have to refine that statement about the error message I'm getting now: > On upload I get the same 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. > > One tool (calldiff.xml) shows as valid tool, but clicking on that tool I get > the message: > > In green box: Error loading tool: [Errno 2] No such file or directory: > '/var/opt/galaxy/g2cmnty/galaxy_toolshed/shed-tool-data/cg_crr_files.loc'. > Below that: Tool not properly loaded. > > The tools displayed as invalid tools just show the 'Tool not properly loaded' > message. > > This is what I got in the main toolshed. I went back to the test toolshed and > uploaded the same tar ball there, none of the tools loaded properly. > Hope this helps. > > Birgit Crain, Ph.D. | Sr. Professional Services Scientist | Complete > Genomics, Inc. > (650) 428-6023 office | (408) 605-3938 mobile > bcr...@completegenomics.com > > > From: Birgit Crain <bcr...@completegenomics.com> > Date: Tuesday, June 19, 2012 8:25 AM > To: Greg Von Kuster <g...@bx.psu.edu> > Cc: "galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edu> > Subject: Re: [galaxy-dev] tool_data_table_config.xml.sample > > Same file structure, but updated files and added the executable and > tool_config.xml.sample for users who install manually. Here's the tar ball. > > 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: Monday, June 18, 2012 5:29 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, > > 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. > > > > 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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