hello,
I am installing galaxy locally.
I tried to upload a ".bam" file and I got this message:
Traceback (most recent call last):
File "/home/user/galaxy_project/tools/data_source/upload.py", line
386, in <module>
__main__()
File "/home/user/galaxy_project/tools/data_source/upload.py", line
375, in __main__
add_file( dataset, registry, json_file, output_path )
File "/home/user/galaxy_project/tools/data_source/upload.py", line
314, in add_file
if link_data_only == 'copy_files' and
datatype.dataset_content_needs_grooming( output_path ):
File "/home/user/galaxy_project/lib/galaxy/datatypes/binary.py",
line 113, in dataset_content_needs_grooming
version = self._get_samtools_version()
File "/home/user/galaxy_project/lib/galaxy/datatypes/binary.py",
line 97, in _get_samtools_version
output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE,
stdout=subprocess.PIPE ).communicate()[1]
File "/usr/lib/python2.7/subprocess.py", line 679, in __init__
errread, errwrite)
File "/usr/lib/python2.7/subprocess.py", line 1259, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory
This file uploaded successfully, to the galaxy on the net.
what can it be?
thanks for your help
merav
___________________________________________________________
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:
http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
