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 . <mer...@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
___________________________________________________________
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