Creating symlinks with normal extensions is a common
approach here where the Galaxy filenames won't work.

Peter

On Fri, Oct 2, 2015 at 10:57 AM, Martin Vickers <mj...@aber.ac.uk> wrote:
>
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> Hi all,
>
> I've been tasked with getting someone's R script working in our galaxy
> installation and I'm struggling to resolve an issue with an bioconductor
> function that appears to not like the galaxy naming convention (e.g.
> dataset_2.dat) for the bam index file.
>
> The R script can run from the command line like this;
>
>     Rscript script.R input1.xls alignment.bam alignment.bai p
>
> so I have created a wrapper using planemo that does this, and that's fine.
>
> The problem is, when I run the script in galaxy, I get the following error
> from R;
>
> Error in value[[3L]](cond) :
>     failed to open BamFile: failed to load BAM index
>     file: /tmp/tmpdP2eBC/files/000/dataset_3.dat
> Calls: f_oGRSeparateStrands ... tryCatch -> tryCatchList -> tryCatchOne ->
> <Anonymous>
> In addition: Warning messages:
> In doTryCatch(return(expr), name, parentenv, handler) :
>     [bam_index_load] fail to load BAM index.
> Execution halted
>
> The function that reads the bam + bai file in the script is;
>
> bam = readGAlignments(file=bam.file, index=bai.file,
> param=ScanBamParam(which=gr.signal))
>
> http://www.rdocumentation.org/packages/GenomicRanges/html/GAlignments.html
>
> In the documentation for this function it states the following;
>
> "file, index, The path to the BAM file to read, and to the index file of the
> BAM file to read, respectively. The latter is given /without/ the '.bai'
> extension. See |scanBam
> <http://www.rdocumentation.org/packages/Rsamtools/functions/scanBam.html>|
> for more information."
>
> I've played around with this a little and from the command line I've been
> successfully able to run the script to completion when the input bam file
> and bai are completely different names;
>
> e.g.
>
> Rscript script.R input1.xls something.bam meh.bai p
>
> but I can't run it if I change the extension, e.g.
>
> Rscript script.R input1.xls something.dat meh.dat p
> Error in value[[3L]](cond) :
>
>     failed to open BamFile: failed to load BAM index
>     file: /tmp/tmpdP2eBC/files/000/dataset_3.dat
> Calls: f_oGRSeparateStrands ... tryCatch -> tryCatchList -> tryCatchOne ->
> <Anonymous>
> In addition: Warning messages:
> In doTryCatch(return(expr), name, parentenv, handler) :
>     [bam_index_load] fail to load BAM index.
> Execution halted
>
>
> Does anyone have any experience of resolving this kind of issue?
>
>
> - --
>
> - --
> Dr. Martin Vickers
>
> Data Manager/HPC Systems Administrator
> Institute of Biological, Environmental and Rural Sciences
> IBERS New Building
> Aberystwyth University
> SY23 3FG
>
> w: http://www.martin-vickers.co.uk/
> e: mj...@aber.ac.uk
> t: 01970 62 2807
>
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>
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