[galaxy-dev] Data manager for ncbi_blast_plus in the main tool shed?

2017-08-15 Thread David Kovalic 
Peter,
Thanks.
Dan,
What is your opinion (what work needs to be done to make this
production-worthy)? Maybe if my chops are up to it I can take a crack…
David


David Kovalic Ph.D.President,Analomephone:+314.496.8808web:www.analome.comemail:

kova...@analome.com






On Fri, Aug 11, 2017 4:58 AM, Peter Cock p.j.a.c...@googlemail.com  wrote:
Hi David,
Daniel Blankenberg wrote one (CC'd):
https://github.com/peterjc/galaxy_blast/tree/master/data_managers/ncbi_blastdb

http://testtoolshed.g2.bx.psu.edu/view/blankenberg/data_manager_example_blastdb_ncbi_update_blastdb

I've never used it in production and don't have enough understandingof it and
the Data Manager framework to understand what if anythingneeds working on.
Locally we have mirrors of the NCBI blast databases (updated with cron),local
databases for organisms of interest - these are all listed in the *.locfiles by
hand.
Separately, our users can and do make their own databases withinGalaxy using
makeblastdb.
Regards,
Peter
On Thu, Aug 10, 2017 at 10:32 PM, David Kovalic   wrote:
Hi,
Does anyone know if a data manager exists in the tool shed for creating and
integrating NCBI BLAST+ indices within galaxy?
I can't seem to find it in the tools shed or searching the internet Surly such a
tool must exist.
Any info would be greatly appreciated.
Thanks,
David


David Kovalic Ph.D.President,Analomephone:+314.496.8808web:www.analome.comemail:

kova...@analome.com

___
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/

Re: [galaxy-dev] Samtools problem in Docker

2017-08-15 Thread Björn Grüning 
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 
> __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 
> __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 > > 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 >>> 
 > 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
>
> ___
> 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

Re: [galaxy-dev] Samtools problem in Docker

2017-08-15 Thread 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 
__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 
__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 
mailto:bjoern.gruen...@gmail.com>> 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 
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

___
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/