Samtools problem in Docker

classic Classic list List threaded Threaded
6 messages Options
| Threaded
Open this post in threaded view
|

Samtools problem in Docker

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/
| Threaded
Open this post in threaded view
|

Re: Samtools problem in Docker

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 <[hidden email]> 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:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/
| Threaded
Open this post in threaded view
|

Re: Samtools problem in Docker

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 <[hidden email]> 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 <[hidden email]> 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:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/
| Threaded
Open this post in threaded view
|

Re: Samtools problem in Docker

Björn Grüning-3
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 <[hidden email]
>> <mailto:[hidden email]>> 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 <[hidden email]
>> <mailto:[hidden email]>> 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:
>   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:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/
| Threaded
Open this post in threaded view
|

Re: Samtools problem in Docker

Deepak Tanwar
Hi Björn,

I tried again from scratch.

1. I have installed galaxy-stable image via Kitematic.
2. I install samtools: package_samtools_1_2 (2015-07-17) iuc
3. I have uploaded the bam file. Error:

Traceback (most recent call last):
  File "/galaxy-central/tools/data_source/upload.py", line 425, in <module>
    __main__()
  File "/galaxy-central/tools/data_source/upload.py", line 413, in __main__
    add_file( dataset, registry, json_file, output_path )
  File "/galaxy-central/tools/data_source/upload.py", line 340, in add_file
    if link_data_only == 'copy_files' and datatype.dataset_content_needs_grooming( output_path ):
  File "/galaxy-central/lib/galaxy/datatypes/binary.py", line 295, in dataset_content_needs_grooming
    version = self._get_samtools_version()
  File "/galaxy-central/lib/galaxy/datatypes/binary.py", line 244, in _get_samtools_version
    raise Exception(message)
Exception: Attempting to use functionality requiring samtools, but it cannot be located on Galaxy's PATH.
4. I restarted the galaxy and the uploaded the bam file. Error:

Traceback (most recent call last):
  File "/galaxy-central/tools/data_source/upload.py", line 425, in <module>
    __main__()
  File "/galaxy-central/tools/data_source/upload.py", line 413, in __main__
    add_file( dataset, registry, json_file, output_path )
  File "/galaxy-central/tools/data_source/upload.py", line 340, in add_file
    if link_data_only == 'copy_files' and datatype.dataset_content_needs_grooming( output_path ):
  File "/galaxy-central/lib/galaxy/datatypes/binary.py", line 295, in dataset_content_needs_grooming
    version = self._get_samtools_version()
  File "/galaxy-central/lib/galaxy/datatypes/binary.py", line 244, in _get_samtools_version
    raise Exception(message)
Exception: Attempting to use functionality requiring samtools, but it cannot be located on Galaxy's PATH.

5. Now, I installed  suite_samtools_1_2 (2015-04-27) devteam and updated the packages. File uploaded successfully!





On Aug 14, 2017, at 16:58, Björn Grüning <[hidden email]> wrote:

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 <[hidden email]
<[hidden email]>> 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 <[hidden email]
<[hidden email]>> 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:
 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:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/
| Threaded
Open this post in threaded view
|

Re: Samtools problem in Docker

Björn Grüning-3
Hi Deepak,

this is still strange. But as a general remark, don't try to install
package_samtools_1_2 or package_* these are deprecated in favor of Conda
packages.

Glad it is working now for you!
Ciao,
Bjoern

On 15.08.2017 16:31, Deepak Tanwar wrote:

> Hi Björn,
>
> I tried again from scratch.
>
> 1. I have installed galaxy-stable image via Kitematic.
> 2. I install samtools: *package_samtools_1_2 (2015-07-17) iuc*
> 3. I have uploaded the bam file. Error:
>
> Traceback (most recent call last): File
> "/galaxy-central/tools/data_source/upload.py", line 425, in <module>
> __main__() File "/galaxy-central/tools/data_source/upload.py", line 413,
> in __main__ add_file( dataset, registry, json_file, output_path ) File
> "/galaxy-central/tools/data_source/upload.py", line 340, in add_file if
> link_data_only == 'copy_files' and
> datatype.dataset_content_needs_grooming( output_path ): File
> "/galaxy-central/lib/galaxy/datatypes/binary.py", line 295, in
> dataset_content_needs_grooming version = self._get_samtools_version()
> File "/galaxy-central/lib/galaxy/datatypes/binary.py", line 244, in
> _get_samtools_version raise Exception(message) Exception: Attempting to
> use functionality requiring samtools, but it cannot be located on
> Galaxy's PATH.
>
> 4. I restarted the galaxy and the uploaded the bam file. Error:
>
> Traceback (most recent call last): File
> "/galaxy-central/tools/data_source/upload.py", line 425, in <module>
> __main__() File "/galaxy-central/tools/data_source/upload.py", line 413,
> in __main__ add_file( dataset, registry, json_file, output_path ) File
> "/galaxy-central/tools/data_source/upload.py", line 340, in add_file if
> link_data_only == 'copy_files' and
> datatype.dataset_content_needs_grooming( output_path ): File
> "/galaxy-central/lib/galaxy/datatypes/binary.py", line 295, in
> dataset_content_needs_grooming version = self._get_samtools_version()
> File "/galaxy-central/lib/galaxy/datatypes/binary.py", line 244, in
> _get_samtools_version raise Exception(message) Exception: Attempting to
> use functionality requiring samtools, but it cannot be located on
> Galaxy's PATH.
>
>
> 5. Now, I installed  *suite_samtools_1_2 (2015-04-27) devteam* and
> updated the packages. File uploaded successfully!
>
>
>
>
>
>> On Aug 14, 2017, at 16:58, Björn Grüning <[hidden email]
>> <mailto:[hidden email]>> wrote:
>>
>> 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 <[hidden email]
>>>> <mailto:[hidden email]>
>>>> <mailto:[hidden email]>> 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 <[hidden email]
>>>> <mailto:[hidden email]>
>>>> <mailto:[hidden email]>> 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:
>>>  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:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/