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<mailto:bcr...@completegenomics.com>


From: Greg Von Kuster <g...@bx.psu.edu<mailto:g...@bx.psu.edu>>
Date: Thursday, June 14, 2012 11:44 AM
To: Birgit Crain 
<bcr...@completegenomics.com<mailto:bcr...@completegenomics.com>>
Cc: "galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>" 
<galaxy-dev@lists.bx.psu.edu<mailto: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<mailto:bcr...@completegenomics.com>


From: Greg Von Kuster <g...@bx.psu.edu<mailto:g...@bx.psu.edu>>
Date: Wednesday, June 13, 2012 6:05 PM
To: Birgit Crain 
<bcr...@completegenomics.com<mailto:bcr...@completegenomics.com>>
Cc: "galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>" 
<galaxy-dev@lists.bx.psu.edu<mailto: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<mailto:bcr...@completegenomics.com>


From: Greg Von Kuster <g...@bx.psu.edu<mailto:g...@bx.psu.edu>>
Date: Wednesday, June 13, 2012 6:09 AM
To: Birgit Crain 
<bcr...@completegenomics.com<mailto:bcr...@completegenomics.com>>
Cc: "galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>" 
<galaxy-dev@lists.bx.psu.edu<mailto: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<mailto:g...@bx.psu.edu>>
Date: Tuesday, June 12, 2012 1:18 PM
To: Birgit Crain 
<bcr...@completegenomics.com<mailto:bcr...@completegenomics.com>>
Cc: "galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>" 
<galaxy-dev@lists.bx.psu.edu<mailto: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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