Hi Nathan,

please try the following.

ln -s /path/to/your/shed_tools/samtools/0.1.19/devteam/what/ever/
/path/to/your/shed_tools/samttools/default

The important part is that it is samtools < 1.0 and that the default
link is a link to the folder in which you find the env.sh file.

I hope this will tell Galaxy how to find samtools for you. Otherwise
simply put the samtools binary into your $PATH.

Cheers and happy new year!
Bjoern

Am 31.12.2014 um 19:49 schrieb Nathan Kipniss:

> Hi All,
>
> New to galaxy here. I'm having an issue uploading bam files into a local
> instance of galaxy. I understand that it requires samtools, and I installed
> the appropriate dependency from the toolshed. However, I get the following
> error:
>
> Traceback (most recent call last):
>   File "/home/galaxy/galaxy-dist/tools/data_source/upload.py", line
> 407, in <module>
>     __main__()
>   File "/home/galaxy/galaxy-dist/tools/data_source/upload.py", line
> 396, in __main__
>     add_file( dataset, registry, json_file, output_path )
>   File "/home/galaxy/galaxy-dist/tools/data_source/upload.py", line
> 324, in add_file
>     if link_data_only == 'copy_files' and
> datatype.dataset_content_needs_grooming( output_path ):
>   File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line
> 147, in dataset_content_needs_grooming
>     version = self._get_samtools_version()
>   File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line
> 129, in _get_samtools_version
>     output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE,
> stdout=subprocess.PIPE ).communicate()[1]
>   File "/usr/lib/python2.7/subprocess.py", line 710, in __init__
>     errread, errwrite)
>   File "/usr/lib/python2.7/subprocess.py", line 1327, in _execute_child
>     raise child_exception
> OSError: [Errno 2] No such file or directory
>
>
> Which leads me to believe something is wrong with the install (can't
> find samtools). The dependency directory is also set. Is there another
> step I'm missing, or is it better to not install dependencies via the
> toolshed?
>
> Best,
> Nathan Kipniss
>
>
>

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