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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