Re: [galaxy-dev] Samtools problem in Docker

2017-08-14 Thread Björn Grüning 
Hi Deepak,

as Peter mentioned the Galaxy Docker container can be used as it is.
Can you provide the original error message from the TS?

Cheers,
Bjoern

On 14.08.2017 18:17, Deepak Tanwar wrote:
> I am using https://hub.docker.com/r/bgruening/galaxy-stable
> 
> I aded path to the samtools because I was getting error after installing
> samtools from toolshed.
> 
> Thank you,
> Deepak
> 
>> On Aug 14, 2017, at 12:10, Peter Cock > > wrote:
>>
>> Galaxy itself uses samtools for many operations, which is different
>> from when samtools is called as a dependency of a tool run by the
>> Galaxy user.
>>
>> However, the Docker image ought to take care of that - can you
>> give more details of which Docker image you are using (URL,
>> version, etc)?
>>
>> Thanks,
>>
>> Peter
>>
>>
>> On Mon, Aug 14, 2017 at 5:08 PM, Deepak Tanwar > > wrote:
>>> Hello everyone,
>>>
>>> I am facing problem in uploading bam files on Galaxy. I am using Docker
>>> image of Galaxy.
>>>
>>> I have installed samtools version 0.1.19 and added it to the path
>>> /tool_deps/samtools/0.1.19/iuc/package_samtools_0_1_19/c9bd782f5342/bin/samtools
>>>
>>> Error: Exception: Attempting to use functionality requiring samtools,
>>> but it
>>> cannot be located on Galaxy's PATH.
>>>
>>> Thank you,
>>> Deepak
>>>
>>> ___
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> 
> 
> 
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Re: [galaxy-dev] Samtools problem in Docker

2017-08-14 Thread Deepak Tanwar 
I am using https://hub.docker.com/r/bgruening/galaxy-stable

I aded path to the samtools because I was getting error after installing 
samtools from toolshed.

Thank you,
Deepak

On Aug 14, 2017, at 12:10, Peter Cock 
mailto:p.j.a.c...@googlemail.com>> wrote:

Galaxy itself uses samtools for many operations, which is different
from when samtools is called as a dependency of a tool run by the
Galaxy user.

However, the Docker image ought to take care of that - can you
give more details of which Docker image you are using (URL,
version, etc)?

Thanks,

Peter


On Mon, Aug 14, 2017 at 5:08 PM, Deepak Tanwar 
mailto:dktan...@hotmail.com>> wrote:
Hello everyone,

I am facing problem in uploading bam files on Galaxy. I am using Docker
image of Galaxy.

I have installed samtools version 0.1.19 and added it to the path
/tool_deps/samtools/0.1.19/iuc/package_samtools_0_1_19/c9bd782f5342/bin/samtools

Error: Exception: Attempting to use functionality requiring samtools, but it
cannot be located on Galaxy's PATH.

Thank you,
Deepak

___
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 https://lists.galaxyproject.org/

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 http://galaxyproject.org/search/

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Re: [galaxy-dev] Samtools problem in Docker

2017-08-14 Thread Peter Cock 
Galaxy itself uses samtools for many operations, which is different
from when samtools is called as a dependency of a tool run by the
Galaxy user.

However, the Docker image ought to take care of that - can you
give more details of which Docker image you are using (URL,
version, etc)?

Thanks,

Peter


On Mon, Aug 14, 2017 at 5:08 PM, Deepak Tanwar  wrote:
> Hello everyone,
>
> I am facing problem in uploading bam files on Galaxy. I am using Docker
> image of Galaxy.
>
> I have installed samtools version 0.1.19 and added it to the path
> /tool_deps/samtools/0.1.19/iuc/package_samtools_0_1_19/c9bd782f5342/bin/samtools
>
> Error: Exception: Attempting to use functionality requiring samtools, but it
> cannot be located on Galaxy's PATH.
>
> Thank you,
> Deepak
>
> ___
> 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/
___
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:
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To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/

[galaxy-dev] Samtools problem in Docker

2017-08-14 Thread Deepak Tanwar 
Hello everyone,

I am facing problem in uploading bam files on Galaxy. I am using Docker image 
of Galaxy.

I have installed samtools version 0.1.19 and added it to the path 
/tool_deps/samtools/0.1.19/iuc/package_samtools_0_1_19/c9bd782f5342/bin/samtools

Error: Exception: Attempting to use functionality requiring samtools, but it 
cannot be located on Galaxy's PATH.

Thank you,
Deepak
___
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/