Creating R galaxy wrapper where a function checks file extension
-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 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 -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.14 (GNU/Linux) iQEcBAEBAgAGBQJWDlUgAAoJEHa0a8GkKQgIpUcIAK9OZ9402FRaROF89b6bO1CY d+KP/X0NCxY+AXEddU3lhXi8O9haaKRA/pmxsGyydP0VQfaCrSSlS9nzhncG6Zav gpXe5NjFkwe8a/qaZTVf0YjlYq0sI81S7QAJnzlKXvYSjcz1xNDE9O4qSHqdhefX oI6GWmR+vHi7CTqNuHwpyY9Qoafd5nls0oQoCYDh9YWrn9GZ8fe1qQ9W7iUli/oT dPMYwWs0OL8NfSCuIcz2Dbr1XMt+o5HpQY/afoGWaq3zz5Ie0NhCLKz34bFps3IW 8K0DEROmCTxsXBa54gnnkhVgCI3zkfFCfa47xp13vT2dJALdzYoT6vDj8aC/mes= =ijgr -----END PGP SIGNATURE-----
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:
-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1
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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___________________________________________________________ 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/
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-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 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) iQEcBAEBAgAGBQJWDlmjAAoJEHa0a8GkKQgIqqkH/RwvFjF//9z3ucrAziYKbuia qe9fFiAUhfgMFYUxVxatdR1CqzLChcONonPDgcouxGO7i1EgGNmoRqYdEdCrHbPF WXpS/1txd8ieIxIp4IjrrozoXnd7x360M6MZd8yh6YxNd+LXQdZyWBAYUePwl5RQ x/rwaJHnfw2hiWtHLWlrqHQJESz4zo1L0Wjymy8ehyvo9zG6760/zZSInaHmFPkN 6YJVmr0o/k1FpQrXNaRlmxMKC9jbPoDvF6ZkpseA9y1ojmFpS0mrBBLxZyaGaru9 iKH4TYnD2PTU5L+2bmCbAiEa7us0KXEx74Mq8WaKQ/hwsvXQiCpXXmvPj7oCFSI= =MVS2 -----END PGP SIGNATURE-----
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:
-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1
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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-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 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)
(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
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 ->
<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 ->
https://github.com/galaxyproject/tools-iuc/blob/master/tools/bedtools/multiC... that's fine. tryCatchOne -> 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) iQEcBAEBAgAGBQJWDnpKAAoJEHa0a8GkKQgIKwgH/0U7reSPcg/45xhMgoqd3XBT kLYiIvg1zufLLw2CEYxci/LD2ZdwvqI+Df3BrsTJgpT3tQxjOWsEHzVkVZfkcS+3 FZDj3v2Pbsb/OFIZIDjbpx0TarKwjNoA2kGW64M9Iuv43gYrGE9Z5iOMuU+2oCHi FKVY1QKiAsVz0opEoXMNjkelSLcdDTA7PDrsxBCFhQl/ck63ZcZZASuZE5TQ0Wda M7x5KxX42gLJ8r8nl1X99XzSUDxvHb4No8quzb058vnu4em4abVKuz0jVmRGKmYh X4P8zpikDYpH116s//5enEe8x+kutooyhPXHX9dDH6LI/+ejAyNUTyeGsOcTmrY= =jAz3 -----END PGP SIGNATURE-----
participants (2)
-
Martin Vickers -
Peter Cock