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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: mjv08@aber.ac.uk
t: 01970 62 2807

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