Re: [galaxy-dev] Changing Tool Shed URL

[Youssef GHORBAL]

Hello,

What worked for us was this action sequence :
- stop Galaxy
- update config/tool_sheds_file.xml (change the URL from the old one to 
the new one)
- “sed” shed_tool_conf.xml to change the “guid", the tool_shed and the 
“file” to replace the old prefix with the new prefix.
- update the tool_version table (the tool_id column) to change the old 
prefix to the new prefix.
- update the tool_shed_repositoriy table to change the tool_shed column 
to use the new tooshed prefix
- update the directory shed_tools to rename the directory from the old 
prefix to the new prefix (care to adapt the subdirectories too : 
./mytoolshed.url/xxx => ./mytoolshed2.url/) 
- start Galaxy (and cross your fingers)

Hope this help !

Youssef Ghorbal
Institut Pasteur
-
> On 20 Oct 2016, at 00:16, Youssef GHORBAL  wrote:
> 
> Hello,
> 
>   I’m wondering if there is any way to change an established Tool Shed 
> URL.
>   I have a Galaxy instance and a Tool Shed instance 
> (http://mytoolshed.url/xxx) A lot of tools have beed installed from that Tool 
> Shed inside Galaxy (tools referenced inside workflows etc)
>   I want to change the Tool Shed URL from http://mytoolshed.url/xxx to 
> http://mytoolshed2.url/. 
> 
>   Galaxy and Tool Shed seems to use parts of the URL as a guid for tools.
>   
>   Tool Shed does not seem to bother to be called by either URLs (it 
> generates guids with the new URLs scheam for new tools though)
> 
>   Galaxy does not seem to handle it, I changed the tool_sheds_conf.xml to 
> point to new URL, but when I update a tool on the Tool Shed, Galaxy gets the 
> new version but it generates buggy tool panel (the tool is cited twice)
>   I also tried to mess around with the shed_tool_conf.xml apdapting the 
> guids and the  items with no luck.
> 
>   Can someone point me to the right direction ? How the matching is done 
> between shed_tool_conf.xml entries, the tool_version and tool_shed_repository 
> tables.
> 
>   Thank you for your help.
> 
> Youssef Ghorbal
> Institut Pasteur
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Re: [galaxy-dev] Data Library Import "Click this to start analyzing it." requires relogin

[D K]

Does anybody have any idea about this? To summarize, if a user imports data
from a shared data library and clicks on the pop-up to start analyzing
their data they are redirected to the login page even though they are
already logged in. Is there a setting to change this?
Thanks

On Sun, Oct 16, 2016 at 8:19 PM, D K  wrote:

> Hi Galaxy-devs,
>
> On my local instance of Galaxy (v16.07) when a user imports a shared data
> library file into their history and clicks on the "Selected datasets
> imported into history. Click this to start analyzing it."  popup, they
> get directed back to the Galaxy log in page regardless if they are already
> logged in. Does this have to do with my settings in galaxy.ini? This
> behavior does not occur on usegalaxy.org. Any suggestions would be
> appreciated.
>
> Thanks!
>
> DK
>
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[galaxy-dev] Wrapper for the MISO programs

[evan clark]

I am currently working to create a wrapper for the MISO tools and wanted 
to see if anyone has previously developed a functional or 
semi-functional wrapper for it.

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Re: [galaxy-dev] user email info

[Marius van den Beek]

Hi Mohamed,

“$__user_email__” is filled in by galaxy when generating the command line,
so you can directly refer to this in your command line.
See 
https://github.com/galaxyproject/tools-iuc/blob/master/tools/tool_factory_2/rgToolFactory2.xml#L12
 

for an example.

Best,
Marius

> On 20 Oct 2016, at 14:55, Mohamed Kassam  wrote:
> 
> Dear all,
> I would like to send as a parameter the name of the user (either user email 
> or username).
> I tried in my xml file the option 
> 
> 
> 
>   
> 
>   
> 
> But  I have in results 
> X__user_email__
> 
> 
> Any clue ?
> 
> 
> Thanks in advance,
> 
> Mohamed
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[galaxy-dev] user email info

[Mohamed Kassam]

Dear all,
I would like to send as a parameter the name of the user (either user email
or username).
I tried in my xml file the option





  

But  I have in results
X__user_email__


Any clue ?


Thanks in advance,

Mohamed
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Re: [galaxy-dev] Tool.xml : correct way to define an environment_variable ?

[Pierre Lindenbaum]

Thanks Peter,
it works, now
I've moved my xml to the way you've suggested **and** I had to change 
the name of my environment_variable. I don't know why but I suspect 
there is a 'ghost/persistent' (?) version of my variable that still 
exists(!?)  somewhere from a previous attempt.


Thank you again.

P.
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Re: [galaxy-dev] Tool.xml : correct way to define an environment_variable ?

[Pierre Lindenbaum]

On 10/20/2016 11:06 AM, Peter Cock wrote:

Hi Pierre,

The first example looks OK, very similar to this one of mine for example,
so I am not sure what is breaking:

https://github.com/peterjc/pico_galaxy/blob/133aea82c02adf5509134c415565ada99c519312/tools/effectiveT3/tool_dependencies.xml

I would try adding more shell actions to debug this with echo statements?

Hi Peter,
Thanks , your xml is inspiring, I'll have a look at this.
Best,

Pierre
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Re: [galaxy-dev] Changing Tool Shed URL

[Marius van den Beek]

This wouldn’t be a transfer, you would uninstall the tools coming from the
old toolshed and re-install them form the new toolshed.
This is only possible if these tools are available from the second toolshed.

To illustrate the procedure, this is what you would do if you would take
all tools from usegalaxy.org,
and replace the tools coming from the main tool shed with the same tools
but coming form the testtoolshed

get-tool-list -g https://usegalaxy.org/ -o tool_list.yml
sed -i .bak 's/toolshed.g2.bx.psu.edu/testtoolshed.g2.bx.psu.edu/g'
tool_list.yml
shed-install -g  -a  -t tool_list.yml

​

On 20 October 2016 at 11:02, Olivia Doppelt-Azeroual <
olivia.dopp...@pasteur.fr> wrote:

> Hello Marius,
>
> Thank you for your answer.
>
> Are you sure that ephemeris can transfer tool from toolshed1 to toolshed2
> ? We read that it was only implemented to install tools from a toolshed on
> a Galaxy.
>
> We will try the second solution and as we already tried to manipulate the
> database, we stongly agree that it is not THE solution.
>
> Cheers,
>
> -
>
> Fabien and Olivia and Youssef
>
>
>
> Le 20/10/2016 à 10:29, Marius van den Beek a écrit :
>
> Hi Youssef,
>
> the tool shed url is also stored in the database, that's why just changing
> the shed_tool_conf.xml is not working. I think you have a bunch of options
> here:
> 1: You can make a list of tools from that toolshed and re-install them
> from the new toolshed.
> https://pypi.python.org/pypi/ephemeris/ is a nice tool to do this
> efficiently.
> Galaxy is (or should be) smart enough to recognize this and will (should)
> not break existing workflows and tool reruns.
> 2: You can setup an alias in your /etc/hosts file if only the toolshed's
> URL has changed, or you can setup a proxy to forward the requests
> if also the subdirectory has changed.
> 3. You can try to manipulate the database directly. (But I would seriously
> advise you to go with possibilities 1 or 2).
>
> Best,
> Marius
>
> On 20 October 2016 at 00:16, Youssef GHORBAL 
> wrote:
>
>> Hello,
>>
>> I’m wondering if there is any way to change an established Tool
>> Shed URL.
>> I have a Galaxy instance and a Tool Shed instance (
>> http://mytoolshed.url/xxx) A lot of tools have beed installed from that
>> Tool Shed inside Galaxy (tools referenced inside workflows etc)
>> I want to change the Tool Shed URL from http://mytoolshed.url/xxx
>> to http://mytoolshed2.url/.
>>
>> Galaxy and Tool Shed seems to use parts of the URL as a guid for
>> tools.
>>
>> Tool Shed does not seem to bother to be called by either URLs (it
>> generates guids with the new URLs scheam for new tools though)
>>
>> Galaxy does not seem to handle it, I changed the
>> tool_sheds_conf.xml to point to new URL, but when I update a tool on the
>> Tool Shed, Galaxy gets the new version but it generates buggy tool panel
>> (the tool is cited twice)
>> I also tried to mess around with the shed_tool_conf.xml apdapting
>> the guids and the  items with no luck.
>>
>> Can someone point me to the right direction ? How the matching is
>> done between shed_tool_conf.xml entries, the tool_version and
>> tool_shed_repository tables.
>>
>> Thank you for your help.
>>
>> Youssef Ghorbal
>> Institut Pasteur
>> ___
>> 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:
>>   https://lists.galaxyproject.org/
>>
>> To search Galaxy mailing lists use the unified search at:
>>   http://galaxyproject.org/search/mailinglists/
>
>
>
>
> ___
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> in your mail client.  To manage your subscriptions to this
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>   http://galaxyproject.org/search/mailinglists/
>
>
> --
> Olivia Doppelt-Azeroual, PhD
> Bioinformatics Engineer
> CIB - C3BI - Institut Pasteur, Paris
>
> Email: olivia.dopp...@pasteur.fr
> Tel: 01 44 38 92 15
>
>
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Re: [galaxy-dev] Changing Tool Shed URL

[Olivia Doppelt-Azeroual]

Hello Marius,

Thank you for your answer.

Are you sure that ephemeris can transfer tool from toolshed1 to 
toolshed2 ? We read that it was only implemented to install tools from a 
toolshed on a Galaxy.


We will try the second solution and as we already tried to manipulate 
the database, we stongly agree that it is not THE solution.


Cheers,

-

Fabien and Olivia and Youssef



Le 20/10/2016 à 10:29, Marius van den Beek a écrit :

Hi Youssef,

the tool shed url is also stored in the database, that's why just changing
the shed_tool_conf.xml is not working. I think you have a bunch of 
options here:
1: You can make a list of tools from that toolshed and re-install them 
from the new toolshed.
https://pypi.python.org/pypi/ephemeris/ 
 is a nice tool to do this 
efficiently.
Galaxy is (or should be) smart enough to recognize this and will 
(should) not break existing workflows and tool reruns.
2: You can setup an alias in your /etc/hosts file if only the 
toolshed's URL has changed, or you can setup a proxy to forward the 
requests

if also the subdirectory has changed.
3. You can try to manipulate the database directly. (But I would 
seriously advise you to go with possibilities 1 or 2).


Best,
Marius

On 20 October 2016 at 00:16, Youssef GHORBAL 
> wrote:


Hello,

I’m wondering if there is any way to change an established
Tool Shed URL.
I have a Galaxy instance and a Tool Shed instance
(http://mytoolshed.url/xxx) A lot of tools have beed installed
from that Tool Shed inside Galaxy (tools referenced inside
workflows etc)
I want to change the Tool Shed URL from
http://mytoolshed.url/xxx to http://mytoolshed2.url/.

Galaxy and Tool Shed seems to use parts of the URL as a
guid for tools.

Tool Shed does not seem to bother to be called by either
URLs (it generates guids with the new URLs scheam for new tools
though)

Galaxy does not seem to handle it, I changed the
tool_sheds_conf.xml to point to new URL, but when I update a tool
on the Tool Shed, Galaxy gets the new version but it generates
buggy tool panel (the tool is cited twice)
I also tried to mess around with the shed_tool_conf.xml
apdapting the guids and the  items with no luck.

Can someone point me to the right direction ? How the
matching is done between shed_tool_conf.xml entries, the
tool_version and tool_shed_repository tables.

Thank you for your help.

Youssef Ghorbal
Institut Pasteur
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--
Olivia Doppelt-Azeroual, PhD
Bioinformatics Engineer
CIB - C3BI - Institut Pasteur, Paris

Email: olivia.dopp...@pasteur.fr
Tel: 01 44 38 92 15

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Re: [galaxy-dev] Changing Tool Shed URL

[Marius van den Beek]

Hi Youssef,

the tool shed url is also stored in the database, that's why just changing
the shed_tool_conf.xml is not working. I think you have a bunch of options
here:
1: You can make a list of tools from that toolshed and re-install them from
the new toolshed.
https://pypi.python.org/pypi/ephemeris/ is a nice tool to do this
efficiently.
Galaxy is (or should be) smart enough to recognize this and will (should)
not break existing workflows and tool reruns.
2: You can setup an alias in your /etc/hosts file if only the toolshed's
URL has changed, or you can setup a proxy to forward the requests
if also the subdirectory has changed.
3. You can try to manipulate the database directly. (But I would seriously
advise you to go with possibilities 1 or 2).

Best,
Marius

On 20 October 2016 at 00:16, Youssef GHORBAL 
wrote:

> Hello,
>
> I’m wondering if there is any way to change an established Tool
> Shed URL.
> I have a Galaxy instance and a Tool Shed instance (
> http://mytoolshed.url/xxx) A lot of tools have beed installed from that
> Tool Shed inside Galaxy (tools referenced inside workflows etc)
> I want to change the Tool Shed URL from http://mytoolshed.url/xxx
> to http://mytoolshed2.url/.
>
> Galaxy and Tool Shed seems to use parts of the URL as a guid for
> tools.
>
> Tool Shed does not seem to bother to be called by either URLs (it
> generates guids with the new URLs scheam for new tools though)
>
> Galaxy does not seem to handle it, I changed the
> tool_sheds_conf.xml to point to new URL, but when I update a tool on the
> Tool Shed, Galaxy gets the new version but it generates buggy tool panel
> (the tool is cited twice)
> I also tried to mess around with the shed_tool_conf.xml apdapting
> the guids and the  items with no luck.
>
> Can someone point me to the right direction ? How the matching is
> done between shed_tool_conf.xml entries, the tool_version and
> tool_shed_repository tables.
>
> Thank you for your help.
>
> Youssef Ghorbal
> Institut Pasteur
> ___
> 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:
>   https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
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[galaxy-dev] Perl module problem with vcftools in conda + new tool

[Peter van Heusden]

Hi there

I'm trying to add a wrapper for the vcftools vcf-consensus tool. There is
an existing tool collection for vcftools in tools-devteam, so I'm add it
there. Wrapper is at:

https://github.com/pvanheus/tools-devteam/tree/master/tool_collections/vcftools/vcftools_consensus

I tested this using:

planemo conda_install .
planemo serve --conda_prefix /home/pvh/miniconda2  --con
da_dependency_resolution

When the tool executes I get the error:

  Fatal error: Exit code 2 () Can't locate Vcf.pm in @INC

Which implies that the PERL5LIB is not being set correctly when the tool
runs.

Using planemo test gives me:

No tests were executed - see Galaxy output for details.

Strangely enough on the pull request the Travis test passes (
https://github.com/galaxyproject/tools-devteam/pull/402).

Any idea how to fix this?

Thanks!
Peter
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[galaxy-dev] dynamic runner and embed_metadata_in_job

[Laure QUINTRIC]

Hi Galaxy users,

As somebody try to run dynamic runner with the option 
embed_metadata_in_job set to False ?


I notice that it works with drmaa runner but not with dynamic.

Here is my job_conf.xmf :




python
my_conf
False



I also set the this parameter in galaxy.ini

retry_metadata_internally = True

But I still have the set_metadata.py script in my jobs.

Thanks for help.

Regards,

Laure

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