Hi GregI 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
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Wednesday, June 13, 2012 6:05 PM
To: Birgit Crain <bcrain@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:
<cgatools.tar.gz>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.txtcgatools/tool_data_table_conf.xml.samplecgatools/datatypes_conf.xmlcgatools/lib/galaxy/datatypes/completegenomics.pycgatools/tool-data/cg_crr_files.loc.samplecgatools/tools/cg_cgatools/listvariants.xmlcgatools/tools/cg_cgatools/junctiondiff.xmlcgatools/tools/cg_cgatools/snpdiff.xmlcgatools/tools/cg_cgatools/calldiff.xmlcgatools/tools/cg_cgatools/testvariants.xmlcgatools/tools/cg_cgatools/varfilter.xmlcgatools/tools/cg_cgatools/listtestvariants.xmlcgatools/tools/cg_cgatools/join.xmlcgatools/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
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Wednesday, June 13, 2012 6:09 AM
To: Birgit Crain <bcrain@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:
-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:
<scripts.tar.gz>___________________________________________________________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 <greg@bx.psu.edu>
Date: Tuesday, June 12, 2012 1:18 PM
To: Birgit Crain <bcrain@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
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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.