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Hi Peter,

That's great, worked perfectly.

Thank you very much,

Martin

On 10/02/2015 11:26 AM, Peter Cock wrote:
> If you have a wrapper script, then you can do it there.
>
> It is also possible in the XML directly by building a composite
> command with && separators (which must be escaped as
> && or using CDATA), e.g.
>
> https://github.com/galaxyproject/tools-devteam/blob/master/tools/samtool_filter2/samtool_filter2.xml
> (nice BAM and BAI example)
>
> https://github.com/galaxyproject/tools-devteam/blob/master/tools/freebayes/freebayes.xml
> (does a lot of symlinks)
>
> https://github.com/galaxyproject/tools-iuc/blob/master/tools/bedtools/multiCov.xml
> (part of a for loop for multiple BAM and BAI files)
>
> Note you can't use <command interpreter="..."> in this
> style as the first command is the shell command ln.
>
> Peter
>
>
> On Fri, Oct 2, 2015 at 11:17 AM, Martin Vickers <mjv08@aber.ac.uk> wrote:
>>
> Hi Peter,
>
> Thanks for the reply. Are there any examples of this in action? Is it done
> in the xml wrapper somewhere or do I need to write a script that does this
> and then call the Rscript?
>
> Cheers,
>
> Martin
>
> On 10/02/2015 11:13 AM, Peter Cock wrote:
> >>> 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 <mjv08@aber.ac.uk> wrote:
> >>>>
> >>> 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?
> >>>
> >>>
> >>>>
> >>>>
> >>>> ___________________________________________________________
> >>>> Please keep all replies on the list by using "reply all"
> >>>> in your mail client.  To manage your subscriptions to this
> >>>> and other Galaxy lists, please use the interface at:
> >>>>   https://lists.galaxyproject.org/
> >>>>
> >>>> To search Galaxy mailing lists use the unified search at:
> >>>>   http://galaxyproject.org/search/mailinglists/
>
>>

- --

- --
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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