[BioC] Using easyRNASeq package: question about BAM/BAI and links to them
Nicolas Delhomme
nicolas.delhomme at umu.se
Tue Nov 26 20:36:55 CET 2013
On 26 Nov 2013, at 19:16, Martin Morgan <mtmorgan at fhcrc.org> wrote:
> On 11/26/2013 10:10 AM, Martin Morgan wrote:
>> On 11/26/2013 09:36 AM, Sylvain Foisy Ph. D. wrote:
>>> Hi,
>>>
>>> On 2013-11-26, at 11:55 AM, Nicolas Delhomme wrote:
>>>
>>>> 1) Is there any possibility that you have circular symlinks, or symlink
>>>> chains? I’m not sure how gracefully R would do with symlink chains.
>>>
>>> Nope, I checked for that.
>>>
>>>> 2) Are there no permission issues on the bam/bai files or a subset of them?
>>>
>>> Nope take 2: both locations are own by me with full r+w permissions
>>>
>>>>
>>>> 3) Could it be that the symlink names are too long? That used to create
>>>> problem in the distant past on some linux distro, but I have not seen it
>>>> occurring in years.
>>>
>>> I made it work when I am in the original location (a single BAM/BAI combo) and
>>> it works so the hypothesis of long paths might be it... I'll see what I can
>>> do to rename my stuff with shorter names.
>>>
>>
>> my guess would be cross-file-system symlinks. Martin
>
> Also, I'm not sure how easyRNASeq does things, but it might be more natural to
> operate on a character() or BamFileList() created with the original file names
> spanning multiple directories. If there are changes in Rsamtools or elsewhere
> that can be made to facilitate that please let me know.
>
It does operate on character and you could provide the recursive = TRUE arguments to the easyRNASeq command. BamFileList is implemented in my Git version of easyRNASeq, which I hope to release soon.
Nico
> Martin
>
>>
>>> Thanks for the time
>>>
>>> Sylvain
>>>
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>>
>>
>
>
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