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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
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 pso 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.datCalls: 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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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 pso 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.datCalls: 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
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_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 pso 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.datCalls: 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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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_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:
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 pso 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.datCalls: 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
galaxy-dev@lists.galaxyproject.org
-
Martin Vickers -
Peter Cock