Re: [galaxy-dev] Modifying a Cloud Cluster Instance

[Lapointe, David]

This is on Amazon I should add.
--
David Lapointe Ph.D.
Sr. Bioinformatics Specialist
Research Technology (RT)
Tufts Technology Services (TTS)
16 Dearborn Road
Somerville MA 02144

Phone:  617-627-5319
Fax: 617-627-3667
http://it.tufts.edu

From: galaxy-dev 
>
 on behalf of David Lapointe 
>
Date: Thursday, August 11, 2016 at 1:44 PM
To: 
"galaxy-dev@lists.galaxyproject.org" 
>
Subject: [galaxy-dev] Modifying a Cloud Cluster Instance

I have  a Cloudman instance up and running, but I would like to add SSL ( I 
have a signed cert and key ) and productionize it.  I see several methods 
documented,but it's not clear which one is preferred: edit in place then 
persist changes and restart  (wiki/Cloudman/CustomizeGalaxyCloud) seems best to 
me. Any advice?

Thanks

David
--
David Lapointe Ph.D.
Sr. Bioinformatics Specialist
Research Technology (RT)
Tufts Technology Services (TTS)
16 Dearborn Road
Somerville MA 02144

Phone:  617-627-5319
Fax: 617-627-3667
http://it.tufts.edu
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[galaxy-dev] Modifying a Cloud Cluster Instance

[Lapointe, David]

I have  a Cloudman instance up and running, but I would like to add SSL ( I 
have a signed cert and key ) and productionize it.  I see several methods 
documented,but it's not clear which one is preferred: edit in place then 
persist changes and restart  (wiki/Cloudman/CustomizeGalaxyCloud) seems best to 
me. Any advice?

Thanks

David
--
David Lapointe Ph.D.
Sr. Bioinformatics Specialist
Research Technology (RT)
Tufts Technology Services (TTS)
16 Dearborn Road
Somerville MA 02144

Phone:  617-627-5319
Fax: 617-627-3667
http://it.tufts.edu
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Re: [galaxy-dev] Travis CI for Galaxy repositories?

[Bjoern Gruening]

Hi Peter,

this error on occurs on push, because only during push to master the TS 
upload is triggered.


This error is directly from the TS and this is the reason you don't see 
it before.


You need to include the tool_data_table_conf.xml.sample in your 
repository, referencing your all_fasta data table.


To make it more obvious planemo should detect this error before 
uploading to the TS.

See here: https://github.com/galaxyproject/planemo/issues/531

Hope this helps,
Bjoern


On 11.08.2016 15:07, Peter van Heusden wrote:

Hi everyone

We maintain a tools collection on Github for tools that are not yet 
(or will never be) added to tools-iuc: 
https://github.com/SANBI-SA/tools-sanbi-uwc


I tried copying the .travis.yml from tools-iuc to our repository, and 
it largely works, except for the planemo upload part, which fails with 
this error:


Repository created
cd '/home/pvh/Documents/code/SANBI/pilon/tools-sanbi-uwc/tools/pilon' 
&& git rev-parse HEAD
cd '/home/pvh/Documents/code/SANBI/pilon/tools-sanbi-uwc/tools/pilon' 
&& git diff --quiet

Could not update pilon
Unexpected response from galaxy: 500: {"content_alert": "", "err_msg": 
"Metadata may have been defined for some items in revision 
'f2477672a950'. Correct the following problems if necessary and reset 
metadata.pilon.xml<\/b> - This file requires an entry in the 
tool_data_table_conf.xml file. Upload a file named 
tool_data_table_conf.xml.sample to the repository that includes the 
required entry to correct this error."}


This is related to the pilon tool in that repo (tools/pilon). The tool 
in question optionally uses a dataset from all_fasta, I'm not sure if 
that is relevant for the error. BTW this error happened on push, not 
on PR.


Any ideas?

Thanks,
Peter


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[galaxy-dev] Travis CI for Galaxy repositories?

[Peter van Heusden]

Hi everyone

We maintain a tools collection on Github for tools that are not yet (or
will never be) added to tools-iuc:
https://github.com/SANBI-SA/tools-sanbi-uwc

I tried copying the .travis.yml from tools-iuc to our repository, and it
largely works, except for the planemo upload part, which fails with this
error:

Repository created
cd '/home/pvh/Documents/code/SANBI/pilon/tools-sanbi-uwc/tools/pilon' &&
git rev-parse HEAD
cd '/home/pvh/Documents/code/SANBI/pilon/tools-sanbi-uwc/tools/pilon' &&
git diff --quiet
Could not update pilon
Unexpected response from galaxy: 500: {"content_alert": "", "err_msg":
"Metadata may have been defined for some items in revision 'f2477672a950'.
Correct the following problems if necessary and reset
metadata.pilon.xml<\/b> - This file requires an entry in the
tool_data_table_conf.xml file. Upload a file named
tool_data_table_conf.xml.sample to the repository that includes the
required entry to correct this error."}

This is related to the pilon tool in that repo (tools/pilon). The tool in
question optionally uses a dataset from all_fasta, I'm not sure if that is
relevant for the error. BTW this error happened on push, not on PR.

Any ideas?

Thanks,
Peter
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