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:

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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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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 &amp;&amp; or using CDATA), e.g.

https://github.com/galaxyproject/tools-devteam/blob/master/tools/samtool_fil... (nice BAM and BAI example)

https://github.com/galaxyproject/tools-devteam/blob/master/tools/freebayes/f... (does a lot of symlinks)

https://github.com/galaxyproject/tools-iuc/blob/master/tools/bedtools/multiC... (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:

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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 -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.14 (GNU/Linux)

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