Unfortunately the ToolShed dependency only provides samtools to individual
Galaxy tools that declare a dependency on it. However, it allows multiple
versions of samtools to be available to different (versions of) Galaxy
This does NOT provide a samtools on $PATH for Galaxy itself, and it needs
it for uploading and indexing BAM files.
On Thursday, January 1, 2015, Nathan Kipniss <nkipniss(a)gmail.com> wrote:
So I checked, and it is not. (type not found).
I will try some of the methods suggested on the admin/config wiki. (
But something I am confused over is why did the install not go "properly"
through the toolshed? Or am I missing something in the directions for
On Wed, Dec 31, 2014 at 10:50 AM, Scott Jeschonek <scottj(a)averesystems.com
> Hi Nathan,
> is samtools executable in the environment path?
> On Dec 31, 2014, at 1:49 PM, Nathan Kipniss <nkipniss(a)gmail.com
> 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
> Traceback (most recent call last):
> File "/home/galaxy/galaxy-dist/tools/data_source/upload.py", line 407, in
> File "/home/galaxy/galaxy-dist/tools/data_source/upload.py", line 396, in
> add_file( dataset, registry, json_file, output_path )
> File "/home/galaxy/galaxy-dist/tools/data_source/upload.py", line 324, in
> 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,
> version = self._get_samtools_version()
> File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line 129,
> output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE,
> 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?
> Nathan Kipniss
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