As part of a warmup, I added a tool for perming eQTL analysis using PANAMA( http://ml.sheffield.ac.uk/qtl/panama/). By default PANAMA writes to stderr and creates a PANAM_results.csv file in the same directory as the input files. I wrote a python wrapper https://bitbucket.org/saketkc/galaxy-central/src/3eb26205af5a0b77fa6177d5ecd... for this. I however also came across how stderr text can be handled in Galaxy : http://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Cstdio.3E.2C_.... and thus wrote a new XML : https://gist.github.com/saketkc/5697388 Apparently the above XML runs too, but I dont get back a CSV. Essentially I need to move the PANAMA_results.csv file to output1. Can this be done without using a wrapper at all , just using the XML files ? Is there a way to nest the commands in the XML so that I could do a <move command> after <panama command> , but how would the paths be specified ? Saket
On Mon, Jun 3, 2013 at 11:53 AM, Saket Choudhary <saketkc@gmail.com> wrote:
As part of a warmup, I added a tool for perming eQTL analysis using PANAMA(http://ml.sheffield.ac.uk/qtl/panama/).
By default PANAMA writes to stderr and creates a PANAM_results.csv file in the same directory as the input files.
I wrote ... XML : https://gist.github.com/saketkc/5697388
Apparently the above XML runs too, but I dont get back a CSV. Essentially I need to move the PANAMA_results.csv file to output1. Can this be done without using a wrapper at all , just using the XML files ?
Is there a way to nest the commands in the XML so that I could do a <move command> after <panama command> , but how would the paths be specified ?
Hi Saket, You could try this (two commands in one shell line), but catching error conditions would be a problem: <command>panama $expression_data $snp_data; mv PANAMA_results.csv $output1</command> In cases like this where the underlying tool is too inflexible to accept an output filename, I would personally use a wrapper script which can handle moving things to the desired location, and raising a clear error if the file was not created. Peter
Hi Saket If you want to redirect the executable's stdout to a new Galaxy dataset you've defined as $output, something like: > '$output' is a workable idiom for a command line AFAIK - you need to escape the redirection '>' character or you'll confuse the xml parser. It's often possible to hack a complex command line (or use configfile to write a script!) but as Peter says, it all boils down to personal preference - they all work. Use whatever you find most convenient but remember you may need to maintain it :) On Mon, Jun 3, 2013 at 9:05 PM, Peter Cock <p.j.a.cock@googlemail.com>wrote:
On Mon, Jun 3, 2013 at 11:53 AM, Saket Choudhary <saketkc@gmail.com> wrote:
As part of a warmup, I added a tool for perming eQTL analysis using PANAMA(http://ml.sheffield.ac.uk/qtl/panama/).
By default PANAMA writes to stderr and creates a PANAM_results.csv file in the same directory as the input files.
I wrote ... XML : https://gist.github.com/saketkc/5697388
Apparently the above XML runs too, but I dont get back a CSV. Essentially I need to move the PANAMA_results.csv file to output1. Can this be done without using a wrapper at all , just using the XML files ?
Is there a way to nest the commands in the XML so that I could do a <move command> after <panama command> , but how would the paths be specified ?
Hi Saket,
You could try this (two commands in one shell line), but catching error conditions would be a problem:
<command>panama $expression_data $snp_data; mv PANAMA_results.csv $output1</command>
In cases like this where the underlying tool is too inflexible to accept an output filename, I would personally use a wrapper script which can handle moving things to the desired location, and raising a clear error if the file was not created.
Peter
Thanks Ross and Peter. That worked. I think I will keep the Python wrapper though, gives me more control :) Saket On 3 June 2013 16:48, Ross <ross.lazarus@gmail.com> wrote:
Hi Saket If you want to redirect the executable's stdout to a new Galaxy dataset you've defined as $output, something like: > '$output' is a workable idiom for a command line AFAIK - you need to escape the redirection '>' character or you'll confuse the xml parser. It's often possible to hack a complex command line (or use configfile to write a script!) but as Peter says, it all boils down to personal preference - they all work. Use whatever you find most convenient but remember you may need to maintain it :)
On Mon, Jun 3, 2013 at 9:05 PM, Peter Cock <p.j.a.cock@googlemail.com>wrote:
On Mon, Jun 3, 2013 at 11:53 AM, Saket Choudhary <saketkc@gmail.com> wrote:
As part of a warmup, I added a tool for perming eQTL analysis using PANAMA(http://ml.sheffield.ac.uk/qtl/panama/).
By default PANAMA writes to stderr and creates a PANAM_results.csv file in the same directory as the input files.
I wrote ... XML : https://gist.github.com/saketkc/5697388
Apparently the above XML runs too, but I dont get back a CSV. Essentially I need to move the PANAMA_results.csv file to output1. Can this be done without using a wrapper at all , just using the XML files ?
Is there a way to nest the commands in the XML so that I could do a <move command> after <panama command> , but how would the paths be specified ?
Hi Saket,
You could try this (two commands in one shell line), but catching error conditions would be a problem:
<command>panama $expression_data $snp_data; mv PANAMA_results.csv $output1</command>
In cases like this where the underlying tool is too inflexible to accept an output filename, I would personally use a wrapper script which can handle moving things to the desired location, and raising a clear error if the file was not created.
Peter
Hi Saket, I haven't looked at this but I noticed the following advice on their web site: If you want to call PANAMA directly from python, just take a look at the PANAMA function inpanama.core.run. Do you have a plan for representing the required incoming expression and snp matrices in Galaxy? AFAIK they need to be from the same subjects - so probably need some thought to make it optimal for a biologist user.... On Tue, Jun 4, 2013 at 8:39 PM, Saket Choudhary <saketkc@gmail.com> wrote:
Thanks Ross and Peter. That worked.
I think I will keep the Python wrapper though, gives me more control :)
Saket
On 3 June 2013 16:48, Ross <ross.lazarus@gmail.com> wrote:
Hi Saket If you want to redirect the executable's stdout to a new Galaxy dataset you've defined as $output, something like: > '$output' is a workable idiom for a command line AFAIK - you need to escape the redirection '>' character or you'll confuse the xml parser. It's often possible to hack a complex command line (or use configfile to write a script!) but as Peter says, it all boils down to personal preference - they all work. Use whatever you find most convenient but remember you may need to maintain it :)
On Mon, Jun 3, 2013 at 9:05 PM, Peter Cock <p.j.a.cock@googlemail.com>wrote:
On Mon, Jun 3, 2013 at 11:53 AM, Saket Choudhary <saketkc@gmail.com> wrote:
As part of a warmup, I added a tool for perming eQTL analysis using PANAMA(http://ml.sheffield.ac.uk/qtl/panama/).
By default PANAMA writes to stderr and creates a PANAM_results.csv file in the same directory as the input files.
I wrote ... XML : https://gist.github.com/saketkc/5697388
Apparently the above XML runs too, but I dont get back a CSV. Essentially I need to move the PANAMA_results.csv file to output1. Can this be done without using a wrapper at all , just using the XML files ?
Is there a way to nest the commands in the XML so that I could do a <move command> after <panama command> , but how would the paths be specified ?
Hi Saket,
You could try this (two commands in one shell line), but catching error conditions would be a problem:
<command>panama $expression_data $snp_data; mv PANAMA_results.csv $output1</command>
In cases like this where the underlying tool is too inflexible to accept an output filename, I would personally use a wrapper script which can handle moving things to the desired location, and raising a clear error if the file was not created.
Peter
-- Ross Lazarus MBBS MPH; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444 http://scholar.google.com/citations?hl=en&user=UCUuEM4AAAAJ
Hi Ross, On 4 June 2013 16:15, Ross <ross.lazarus@gmail.com> wrote:
Hi Saket, I haven't looked at this but I noticed the following advice on their web site:
If you want to call PANAMA directly from python, just take a look at the PANAMA function inpanama.core.run.
Do you have a plan for representing the required incoming expression and snp matrices in Galaxy?
Yes, using the API makes more sense. Currently I am relying on the end user to choose the proper set of files to run PANAMA. AFAIK they need to be from the same subjects - so probably need some
thought to make it optimal for a biologist user....
I think this will possibly require the user to upload the dataset with proper naming. say : <mydata>_expression.csv and <mydata>_snp.csv Is there a way in Galaxy to restrict this kind of thing ? I am not sure though, that forcing such constraints will make sense, this is just a suggestion. But as you correctly pointed out, there is a need to organise the data to ensure the correct dataset is fed to PANAMA or for that matter the other tools I am working on. Saket
On Tue, Jun 4, 2013 at 8:39 PM, Saket Choudhary <saketkc@gmail.com> wrote:
Thanks Ross and Peter. That worked.
I think I will keep the Python wrapper though, gives me more control :)
Saket
On 3 June 2013 16:48, Ross <ross.lazarus@gmail.com> wrote:
Hi Saket If you want to redirect the executable's stdout to a new Galaxy dataset you've defined as $output, something like: > '$output' is a workable idiom for a command line AFAIK - you need to escape the redirection '>' character or you'll confuse the xml parser. It's often possible to hack a complex command line (or use configfile to write a script!) but as Peter says, it all boils down to personal preference - they all work. Use whatever you find most convenient but remember you may need to maintain it :)
On Mon, Jun 3, 2013 at 9:05 PM, Peter Cock <p.j.a.cock@googlemail.com>wrote:
On Mon, Jun 3, 2013 at 11:53 AM, Saket Choudhary <saketkc@gmail.com> wrote:
As part of a warmup, I added a tool for perming eQTL analysis using PANAMA(http://ml.sheffield.ac.uk/qtl/panama/).
By default PANAMA writes to stderr and creates a PANAM_results.csv file in the same directory as the input files.
I wrote ... XML : https://gist.github.com/saketkc/5697388
Apparently the above XML runs too, but I dont get back a CSV. Essentially I need to move the PANAMA_results.csv file to output1. Can this be done without using a wrapper at all , just using the XML files ?
Is there a way to nest the commands in the XML so that I could do a <move command> after <panama command> , but how would the paths be specified ?
Hi Saket,
You could try this (two commands in one shell line), but catching error conditions would be a problem:
<command>panama $expression_data $snp_data; mv PANAMA_results.csv $output1</command>
In cases like this where the underlying tool is too inflexible to accept an output filename, I would personally use a wrapper script which can handle moving things to the desired location, and raising a clear error if the file was not created.
Peter
-- Ross Lazarus MBBS MPH; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444 http://scholar.google.com/citations?hl=en&user=UCUuEM4AAAAJ
participants (3)
-
Peter Cock -
Ross -
Saket Choudhary