Is there something helpful in your paster log about the cause?

On Apr 23, 2012, at 4:34 PM, Gregory Miles wrote:

> Thanks again for the feedback...one final (hopefully) thing....as I
> mentioned in first e-mail, we are trying to add a large (~170 GB) BAM
> file to a library with just a link to the file (no copying). After at
> least an hour of working, I get the error message "Unable to finish
> job,
> tool error". Any thoughts as to how I can fix this? Thanks.
> 
> Greg
> 
> 
> On 4/23/12, Greg Von Kuster <g...@bx.psu.edu> wrote:
>> Hi Greg,
>> 
>> Even though you are not copying the data into Galaxy's default data store,
>> Galaxy determines and stores certain metadata for each of the data files to
>> which you are linking. One of the types of metadata defined for the Bam
>> datatypes is it's index, which is created by a call to samtools.
>> 
>> Unfortunately there is really no way around this because Galaxy requires the
>> index file to be in a correct state, and I believe the test to determine
>> correctness is at least as intensive as generating the index in the first
>> place.  It's been a while since I was involved in this (specifically setting
>> metadata for bam files using samtools), so perhaps samtools has been
>> recently improved in this regard.  if so, I'll look to others to let me know
>> I'm now "outdated" in my understanding of this.  If we need to update
>> samtools used by the Galaxy code to take advantage of newer features, we can
>> certainly do so.
>> 
>> Greg Von Kuster
>> 
>> On Apr 23, 2012, at 2:51 PM, Gregory Miles wrote:
>> 
>>> Thank you very much for your help with this - we got that settled. One
>>> other question...we are importing sorted, indexed bam files into a galaxy
>>> data library and we are not having galaxy copy over the files (they are
>>> large) but rather just setting up galaxy such that it points to the
>>> relevant directory. We noticed that the file (160 GB in size) is taking a
>>> long time to import considering all it should be doing is creating a link.
>>> When we examined processes that are running, we noticed that samtools is
>>> running. From searching around a bit, it seems that Galaxy does this in
>>> order to groom the bam file (sort/index) and ensure that it is in the
>>> format necessary for galaxy to be able to interpret it. Is there any way
>>> around this? We did the sorting and indexing prior to import and it's
>>> taking quite a while to perform an unnecessary function. Thanks.
>>> 
>>> Greg
>>> 
>>> Dr. Gregory Miles
>>> Bioinformatics Specialist
>>> Cancer Institute of New Jersey @ UMDNJ
>>> Office: (732) 235 8817
>>> 
>>> -----------------------------------------------------------------------------------------------------------------------------
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>>> 
>>> On Mon, Apr 23, 2012 at 12:55 PM, Greg Von Kuster <g...@bx.psu.edu>
>>> wrote:
>>> Hi Greg,
>>> 
>>> Upload your files to a Galaxy data library using a combination of "Upload
>>> files from filesystem paths" without copying data into Galaxy's default
>>> data store.
>>> 
>>> See the following wiki for all the details:
>>> 
>>> http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files
>>> 
>>> For all of the details about data libraries, see:
>>> 
>>> http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries
>>> 
>>> Greg Von Kuster
>>> 
>>> 
>>> On Apr 23, 2012, at 11:26 AM, Gregory Miles wrote:
>>> 
>>>> We have large files that cannot be uploaded using the "file upload"
>>>> command and instead would need to be uploaded using a URL.
>>>> Unfortunately, we are using a "local" install on a non-local machine, so
>>>> setting up an FTP server on this machine is a security issue. The files
>>>> are located on this computer already anyhow, and Galaxy would simply be
>>>> copying from one folder to another in order to perform the "get data"
>>>> step. Is there a simple way to have a "pointer" of some sort such that
>>>> galaxy knows where this file is and:
>>>> 
>>>> 1) Would not have to copy it and could simply refer to the file
>>>> location.
>>>> 2) Could perform data analysis steps on this file and push the output to
>>>> the usual location (not the location of the data files).
>>>> 
>>>> Any help would be greatly appreciated. Thanks.
>>>> 
>>>> Dr. Gregory Miles
>>>> Bioinformatics Specialist
>>>> Cancer Institute of New Jersey @ UMDNJ
>>>> Office: (732) 235 8817
>>>> 
>>>> -----------------------------------------------------------------------------------------------------------------------------
>>>> CONFIDENTIALITY NOTICE: This email communication may contain private,
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>>>> ___________________________________________________________
>>>> The Galaxy User list should be used for the discussion of
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>>> 
>> 
>> 
> 
> 
> -- 
> 
> Dr. Gregory Miles
> Bioinformatics Specialist
> Cancer Institute of New Jersey @ UMDNJ
> Office: (732) 235 8817
> 
> -----------------------------------------------------------------------------------------------------------------------------
> CONFIDENTIALITY NOTICE: This email communication may contain private,
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> ___________________________________________________________
> The Galaxy User list should be used for the discussion of
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