2013/5/29 Ross <ross.lazarus@gmail.com>

Hi, Merav.
A fully functional Galaxy server relies on a lot of third party software and the error message you see is probably because you do not have samtools available - the upload process needs it to make an index for your bam file.

So the solution may be to install the samtools package - eg for ubuntu something like:
sudo apt-get install samtools

After that, if you execute
samtools

at a console, you should see something like:

rlazarus@iaas1-int:~$ samtools

Program: samtools (Tools for alignments in the SAM format)
Version: 0.1.18 (r982:295)

Usage: samtools <command> [options]

Command: view SAM<->BAM conversion
sort sort alignment file
mpileup multi-way pileup

Please take a look at http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies

On Wed, May 29, 2013 at 8:00 PM, מירב . <mermam@gmail.com> wrote:

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

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--
Ross Lazarus MBBS MPH;
Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444
http://scholar.google.com/citations?hl=en&user=UCUuEM4AAAAJ