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 <bjoern.gruening@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 <p.j.a.cock@googlemail.com
<mailto:p.j.a.cock@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 <dktanwar@hotmail.com
<mailto:dktanwar@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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