[galaxy-dev] samtools

[Beginner TI]

Hi All,

I compiled samtools from source, and just realized that I don't have those
tool xml files. Tried to google but failed to find any samtools wrapper.
This is quite surprising since the main instance has it. Does anyone happen
to know where we could obtain those files that are used by galaxy main
instance? I don't want to use tool_shed and prefer to install all tools
manually. In that case, how could I access the tool xml files that are used
by tool_shed installation process?

Thanks,
Rui
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Re: [galaxy-dev] Docker ToolShed Imports Issue

[Björn Grüning]

Hi Miuki,

can you please show use your tool.yaml file?

Thanks,
Bjoern

Am 18.08.2016 um 16:31 schrieb Yip, Miu ki:
> Hi all,
> 
> I’m trying to import shed tools into Galaxy for Docker. When I build the 
> container, I get this error message:
> 
> TASK [galaxy_tools : Install Tool Shed tools] 
> **
>  [WARNING]: The loop variable 'item' is already in use. You should set the
> `loop_var` value in the `loop_control` option for the task to something else 
> to
> avoid variable collisions and unexpected behavior.
> failed: [localhost] (item={u'owner': u'vlefort', u'tool_shed_url': 
> u'https://toolshed.g2.bx.psu.edu', 
> u'tool_panel_section_label': u'Import Files', u'name': u'phyml'}) => 
> {"changed": false, "cmd": ["/tmp/venv/bin/python", 
> "install_tool_shed_tools.py", "-y", "name: phyml\nowner: 
> vlefort\ntool_panel_section_label: Import Files\ntool_shed_url: 
> https://toolshed.g2.bx.psu.edu\n;, "-a", "admin", "-g", "localhost:8080"], 
> "delta": "0:00:00.781449", "end": "2016-08-17 23:48:07.389199", "failed": 
> true, "failed_when_result": true, "item": {"name": "phyml", "owner": 
> "vlefort", "tool_panel_section_label": "Import Files", "tool_shed_url": 
> "https://toolshed.g2.bx.psu.edu"}, "rc": 0, "start": "2016-08-17 
> 23:48:06.607750", "stderr": "(1/1) Installing tool phyml from vlefort to 
> section \"Import Files\" at revision f6dadc1de75f (TRT: 
> 0:00:00.308611)\r\n\t* Error installing a tool (after phyml)! Name: 
> 0:00:00.247213,owner: vlefort, revision: f6dadc1de75f, error: {\"err_msg\": 
> \"Missing required parameter 'shed_tool_conf'.\", \"err_code\": 
> 47}\r\nInstalled tools (0): []\r\nSkipped tools (0): []\r\nErrored tools 
> (1): [('phyml', u'f6dadc1de75f')]\r\nAll tools listed in 'None' have been 
> processed.\r\nTotal run time: 0:00:00.556216", "stdout": "", "stdout_lines": 
> [], "warnings": []}
> …ignoring
> 
> Is this a conf file issue?
> 
> Best,
> Miuki
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Re: [galaxy-dev] several versions of compiler

[Nikolaos Tur]

Hi,

On Fri, Sep 23, 2016 at 2:13 PM, Björn Grüning 
wrote:

> Hi,
>
> Am 23.09.2016 um 10:42 schrieb Nikolaos Tur:
> > Hi,
> >
> > maybe this was discussed or documented already but I'm lost. How to tell
> > installed tools by tool_shed that I have newer version of gcc and pls
> > use that one instead of default?
>
> Do you want to recompile all tools installed from the TS with a new GCC
> version?
>

just only one which requires more recent version of gcc

Nikolaos
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Re: [galaxy-dev] how to make an exact clone of the usegalaxy.org

[Enis Afgan]

Hi Rui,
You can also take a look at this repo https://github.com/
ARTbio/GalaxyKickStart, and in particular this bit
https://github.com/ARTbio/GalaxyKickStart/tree/master/
extra-files/cloud_setup.

We used this to build standalone Galaxy images on the Jetstream and Google
clouds with a toolset that's as close to Main as one can get without
debugging a number of failed tool installs. Even though it's primarily used
for a cloud image setup, there is no reason for it cannot be used for a
local machine or a VM.

On Mon, Sep 26, 2016 at 11:06 AM, Martin Čech  wrote:

> The link in the first answer is not up to date because things moved,
> however it should be probably linking to here https://github.com/galaxy
> project/ephemeris/blob/master/ephemeris/shed_install.py
>
> Martin
>
> On Mon, Sep 26, 2016 at 11:02 AM Beginner TI  wrote:
>
>> Hi Martin,
>>
>> Thanks!
>>
>> The first link doesn't really work...upon going to github it gave me 404.
>> After I explored a bit more
>> it says itself that it may not work now. :-(
>>
>> However the second one looks quite promising!
>>
>> Cheers,
>> Rui
>>
>> On Mon, Sep 26, 2016 at 7:55 AM, Martin Čech  wrote:
>>
>>> Hi Rui,
>>>
>>> there is no 'mirror' button to obtain Main's toolset yet, but many
>>> pieces are in place to help you with this.
>>>
>>> Please see the following answers for guides and links:
>>>
>>> https://biostar.usegalaxy.org/p/11338/
>>> https://biostar.usegalaxy.org/p/19660/
>>>
>>> Thanks,
>>>
>>> Martin
>>>
>>>
>>>
>>>
>>>
>>> On Mon, Sep 26, 2016 at 10:50 AM Beginner TI 
>>> wrote:
>>>
 Hey Guys,

 I have seen this question being asked quite some times, but there
 wasn't any definitive answers. Today I'm doing a new local install. Upon
 getting the latest github repo, I still only got a small portion of galaxy
 main. Is there any way to include all the tools there automatically?

 Thanks,
 Rui
 ___
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>>>
>>>
>>
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[galaxy-dev] trying to add a new controller to webapps/galaxy/controllers

[Nikolay Aleksandrov Vazov]

Hi,


I am trying to add a new controller (an extension of User class and living in 
the same directory as user.py) to Galaxy. I am trying to call it from within 
user/login.mako by setting :


form_action = h.url_for( controller='NEWCONTROLLER', action='login', 
use_panels=use_panels )


but Galaxy refuses to see it.


In the paster.log I see that the controller is enabled. It is completely 
identical to user.py, just a couple of modified functions bearing the same 
names.


Is there something more to set up to make it accessible from the mako file?


My version os 16.04


Thank you


Nikolay

===
Nikolay Vazov, PhD
Department for Research Computing, University of Oslo
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[galaxy-dev] howto add a controller to Galaxy (sorry for multiple posts)

[Nikolay Aleksandrov Vazov]

Hi,


I am trying to add a new controller (an extension of User class and living in 
the same directory as user.py) to Galaxy. I am trying to call it from within 
user/login.mako by setting :


form_action = h.url_for( controller='NEWCONTROLLER', action='login', 
use_panels=use_panels )


but Galaxy refuses to see it.


In the paster.log I see that the controller is enabled. It is completely 
identical to user.py, just a couple of modified functions bearing the same 
names.


Is there something more to set up to make it accessible from the mako file?


My version os 16.04


Thank you


Nikolay


===
Nikolay Vazov, PhD
Department for Research Computing, University of Oslo
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Re: [galaxy-dev] how to make an exact clone of the usegalaxy.org

[Martin Čech]

The link in the first answer is not up to date because things moved,
however it should be probably linking to here
https://github.com/galaxyproject/ephemeris/blob/master/ephemeris/shed_install.py

Martin

On Mon, Sep 26, 2016 at 11:02 AM Beginner TI  wrote:

> Hi Martin,
>
> Thanks!
>
> The first link doesn't really work...upon going to github it gave me 404.
> After I explored a bit more
> it says itself that it may not work now. :-(
>
> However the second one looks quite promising!
>
> Cheers,
> Rui
>
> On Mon, Sep 26, 2016 at 7:55 AM, Martin Čech  wrote:
>
>> Hi Rui,
>>
>> there is no 'mirror' button to obtain Main's toolset yet, but many pieces
>> are in place to help you with this.
>>
>> Please see the following answers for guides and links:
>>
>> https://biostar.usegalaxy.org/p/11338/
>> https://biostar.usegalaxy.org/p/19660/
>>
>> Thanks,
>>
>> Martin
>>
>>
>>
>>
>>
>> On Mon, Sep 26, 2016 at 10:50 AM Beginner TI 
>> wrote:
>>
>>> Hey Guys,
>>>
>>> I have seen this question being asked quite some times, but there wasn't
>>> any definitive answers. Today I'm doing a new local install. Upon getting
>>> the latest github repo, I still only got a small portion of galaxy main. Is
>>> there any way to include all the tools there automatically?
>>>
>>> Thanks,
>>> Rui
>>> ___
>>> 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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Re: [galaxy-dev] samtools

[Martin Čech]

Hi Rui,

you can install the following suite which includes about a dozen of wrapped
samtools.

https://toolshed.g2.bx.psu.edu/view/devteam/suite_samtools_1_2/5b673ccc8747

Martin

On Mon, Sep 26, 2016 at 11:05 AM Beginner TI  wrote:

> I did see that if I click each individual tool, and then in the options, I
> could find the tool xml file, but this would require manually clicking each
> of it. Is there any way we could get these in batch? I shouldn't be the
> first or last person that want to make an identical clone of main galaxy
> instance, so I assume that there are some good/easy ways I'm missing?
>
> thanks,
> Rui
>
> On Sun, Sep 25, 2016 at 1:05 AM, Beginner TI  wrote:
>
>> Hi All,
>>
>> I compiled samtools from source, and just realized that I don't have
>> those tool xml files. Tried to google but failed to find any samtools
>> wrapper. This is quite surprising since the main instance has it. Does
>> anyone happen to know where we could obtain those files that are used by
>> galaxy main instance? I don't want to use tool_shed and prefer to install
>> all tools manually. In that case, how could I access the tool xml files
>> that are used by tool_shed installation process?
>>
>> Thanks,
>> Rui
>>
>
> ___
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Re: [galaxy-dev] samtools

[Beginner TI]

I did see that if I click each individual tool, and then in the options, I
could find the tool xml file, but this would require manually clicking each
of it. Is there any way we could get these in batch? I shouldn't be the
first or last person that want to make an identical clone of main galaxy
instance, so I assume that there are some good/easy ways I'm missing?

thanks,
Rui

On Sun, Sep 25, 2016 at 1:05 AM, Beginner TI  wrote:

> Hi All,
>
> I compiled samtools from source, and just realized that I don't have those
> tool xml files. Tried to google but failed to find any samtools wrapper.
> This is quite surprising since the main instance has it. Does anyone happen
> to know where we could obtain those files that are used by galaxy main
> instance? I don't want to use tool_shed and prefer to install all tools
> manually. In that case, how could I access the tool xml files that are used
> by tool_shed installation process?
>
> Thanks,
> Rui
>
___
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Re: [galaxy-dev] how to make an exact clone of the usegalaxy.org

[Beginner TI]

Hi Martin,

Thanks!

The first link doesn't really work...upon going to github it gave me 404.
After I explored a bit more
it says itself that it may not work now. :-(

However the second one looks quite promising!

Cheers,
Rui

On Mon, Sep 26, 2016 at 7:55 AM, Martin Čech  wrote:

> Hi Rui,
>
> there is no 'mirror' button to obtain Main's toolset yet, but many pieces
> are in place to help you with this.
>
> Please see the following answers for guides and links:
>
> https://biostar.usegalaxy.org/p/11338/
> https://biostar.usegalaxy.org/p/19660/
>
> Thanks,
>
> Martin
>
>
>
>
>
> On Mon, Sep 26, 2016 at 10:50 AM Beginner TI  wrote:
>
>> Hey Guys,
>>
>> I have seen this question being asked quite some times, but there wasn't
>> any definitive answers. Today I'm doing a new local install. Upon getting
>> the latest github repo, I still only got a small portion of galaxy main. Is
>> there any way to include all the tools there automatically?
>>
>> Thanks,
>> Rui
>> ___
>> 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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Re: [galaxy-dev] how to make an exact clone of the usegalaxy.org

[Martin Čech]

Hi Rui,

there is no 'mirror' button to obtain Main's toolset yet, but many pieces
are in place to help you with this.

Please see the following answers for guides and links:

https://biostar.usegalaxy.org/p/11338/
https://biostar.usegalaxy.org/p/19660/

Thanks,

Martin





On Mon, Sep 26, 2016 at 10:50 AM Beginner TI  wrote:

> Hey Guys,
>
> I have seen this question being asked quite some times, but there wasn't
> any definitive answers. Today I'm doing a new local install. Upon getting
> the latest github repo, I still only got a small portion of galaxy main. Is
> there any way to include all the tools there automatically?
>
> Thanks,
> Rui
> ___
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> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
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>
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>   http://galaxyproject.org/search/mailinglists/
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[galaxy-dev] how to make an exact clone of the usegalaxy.org

[Beginner TI]

Hey Guys,

I have seen this question being asked quite some times, but there wasn't
any definitive answers. Today I'm doing a new local install. Upon getting
the latest github repo, I still only got a small portion of galaxy main. Is
there any way to include all the tools there automatically?

Thanks,
Rui
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[galaxy-dev] Recommended torque version?

[Fourie Joubert]

Hi Folks

Any recommendations for the best torque version to install on a new 
setup, that plays well with pbs_python-4.4.0?


Thanks and regards!

Fourie

--
--
Prof Fourie Joubert
Centre for Bioinformatics and Computational Biology
Genomics Research Institute
University of Pretoria
fourie.joub...@up.ac.za
http://www.bi.up.ac.za
Tel. +27-12-420-5825
Fax. +27-12-420-5800

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This message and attachments are subject to a disclaimer. Please refer
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