Question: Problem to upload dataset in Galaxy local
gravatar for b.roux
4.3 years ago by
United Kingdom
b.roux10 wrote:


I've recently installed galaxy locally on my computer, I got it run but I can't upload dataset. My dataset (BAM) are really big (~40 GB each), so I tried to set up 'upload directory of files'. I created a folder outside of galaxy-dist and inserting the right path in the universe_wsgi.ini: library_import_dir = /Users/br237/import

Every time the loading fails with this error message:

Traceback (most recent call last):
  File "/Users/br237/galaxy-dist/tools/data_source/", line 394, in 
  File "/Users/br237/galaxy-dist/tools/data_source/", line 383, in __main__
    add_file( dataset, registry, json_file, output_path )
  File "/Users/br237/galaxy-dist/tools/data_source/", line 322, in add_file
    if link_data_only == 'copy_files' and datatype.dataset_content_needs_grooming( output_path ):
  File "/Users/br237/galaxy-dist/lib/galaxy/datatypes/", line 148, in dataset_content_needs_grooming
    version = self._get_samtools_version()
  File "/Users/br237/galaxy-dist/lib/galaxy/datatypes/", line 130, in _get_samtools_version
    output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE, stdout=subprocess.PIPE ).communicate()[1]
  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/", line 711, in __init__
    errread, errwrite)
  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/", line 1308, in _execute_child
    raise child_exception
OSError: [Errno 2] No such file or directory


Any suggestions why is it crashing all the time?

Many thanks


upload galaxy dataset • 1.7k views
ADD COMMENTlink modified 4.3 years ago • written 4.3 years ago by b.roux10
gravatar for Wolfgang Maier
4.3 years ago by
Wolfgang Maier600 wrote:

When you import a bam file, Galaxy is trying to call samtools to access the file's content (to "groom" it as it's called in Galaxy).

What looks like an upload issue, is really one with locating the samtools executable, which could be either because you haven't installed it or because it's in a directory that's not in your system PATH.


ADD COMMENTlink written 4.3 years ago by Wolfgang Maier600
gravatar for b.roux
4.3 years ago by
United Kingdom
b.roux10 wrote:

Hi Wolfgang

Thanks for your reply. I have set up the tool_dependency_dir and I think it's working fine. I mean, I get a message that the tools are installed and I can see them appearing on my tool tab. I installed some samtools and tried to import some dataset without success. I am getting the exact error message than above. Maybe I haven't installed the right ones, though. Is there a specific samtool to install? Or is there something else to look for?

I don't know if it's related or if it could help but I've noticed a strange message in my terminal when I launch galaxy:

File "/Users/br237/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/", line 576, in parse

    source = open(source, "rb")

IOError: [Errno 2] No such file or directory: './tools/mutation/visualize.xml' INFO 2014-08-06 12:42:34,612 Parsing the tool configuration ./shed_tool_conf.xml

Many thanks

ADD COMMENTlink written 4.3 years ago by b.roux10

hmm, so what do you mean by you installed some samtools: directly on your system? through the toolshed?

What happens if you simply type:


in a terminal ?

If that appears to work, try:

which samtools

to see where that executable resides, then check if the location is in your PATH environmental variable.

ADD REPLYlink written 4.3 years ago by Wolfgang Maier600

Hi Wolf

Thanks for your help. It was indeed a problem with the PATH and my samtools. It took me a while to work out how to change the PATH (I'm just a novice in galaxy/programming), but I finally managed to do it!

Thanks again


ADD REPLYlink written 4.3 years ago by b.roux10
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