Hi all,

I think I have fallen over the same problem Glen Beane reported in Nov 2010,
http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-November/003943.html

I recall from reading the mailing list, that when you import a BAM file
into Galaxy, it gets sorted and indexed. That makes sense since most
tools need that to be done, and resorting an already sorted file should
be quick.

However, I'm trying to import some presorted and indexed BAM files
into a library in Galaxy via the Admin settings, linking to the file not
copying it. I'm getting this:

<quote>

File size: 4.4 Gb
Data type: auto
Build: ?
Miscellaneous information: uploaded bam fileTraceback (most recent
call last): File "/opt/galaxy-dist/tools/data_source/upload.py", line
447, in __main__() File
"/opt/galaxy-dist/tools/data_source/upload.py", line 439, in __main__
add_file( dataset, registry, j
Job Standard Output

[bam_sort_core] merging from 28 files...

Job Standard Error

Traceback (most recent call last):
  File "/opt/galaxy-dist/tools/data_source/upload.py", line 447, in
    __main__()
  File "/opt/galaxy-dist/tools/data_source/upload.py", line 439, in __main__
    add_file( dataset, registry, json_file, output_path )
  File "/opt/galaxy-dist/tools/data_source/upload.py", line 381, in add_file
    datatype.groom_dataset_content( output_path )
  File "/opt/galaxy-dist/lib/galaxy/datatypes/binary.py", line 98, in
groom_dataset_content
    shutil.move( samtools_created_sorted_file_name, file_name )
  File "/usr/local/lib/python2.6/shutil.py", line 260, in move
    copy2(src, real_dst)
  File "/usr/local/lib/python2.6/shutil.py", line 95, in copy2
    copyfile(src, dst)
  File "/usr/local/lib/python2.6/shutil.py", line 51, in copyfile
    with open(dst, 'wb') as fdst:
IOError: [Errno 13] Permission denied: '/data/XXX-bwa-out.sorted.bam'

error
Database/Build: ?
Number of data lines: None
Disk file: /data/XXX-bwa-out.sorted.bam

</quote>

Clearly from the error message, Galaxy is trying to edit the source
file (and the Unix account it is running in only has read permission
for this file and its containing folder). From the stdout message
"[bam_sort_core] merging from 28 files..." it looks like Galaxy is
trying to (re)sort my file, and may well attempt to reindex it. Is that
likely to be the case?

If the "copy" option had been used, then sorting and indexing
should work - but I want Galaxy to link to the file as it it.

If however "copy" was not selected, then I don't want Galaxy
trying to alter the file like this. Could the sort+index be disabled
in this mode? I think it is reasonable to expect administrators
trying to import BAM files from the local file system to take
care of this.

Alternatively, you could actually check if the BAM file is pre-sorted
or not.

Peter
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