10:15 a.m.
On Tue, Oct 12, 2010 at 10:43 AM, Freddy <freddy.debree(a)wur.nl> wrote:
Hi Peter,
Running R from xml is not so straight forward to me.
Is the interpreter "bash" or is it "R"?
If "bash"
then it should be running "R --vanilla --slave input < Rscript >
output"
if "R"
then it should be running ? smthg like "source(Rscript)"
Hope you can help...
Freddy
Consider a simple R script, hello_world.R like this:
print('Hello world');
print(commandArgs());
Then in Galaxy I think you'd need the default interpreter
("bash") and the command to be:
R --vanilla --file=hello_world.R --args "Args go here"
I'm assuming your script will write useful output to a
file, and stdout can be discarded.
However, what I originally had in mind was setting the
hash bang and executable bit with chmod so that you
can do this at the command line:
./hello_world.R "Args go here"
Once that works, calling it from Galaxy should be trivial.
I think one way to do this is with the little r package:
http://code.google.com/p/littler/
Peter
10:28 a.m.
New subject: rpy or perl
On Tue, Oct 12, 2010 at 11:15 AM, Peter <peter(a)maubp.freeserve.co.uk> wrote:
On Tue, Oct 12, 2010 at 10:43 AM, Freddy <freddy.debree(a)wur.nl>
wrote:
>
>
> Hi Peter,
>
> Running R from xml is not so straight forward to me.
> Is the interpreter "bash" or is it "R"?
> If "bash"
> then it should be running "R --vanilla --slave input < Rscript >
> output"
> if "R"
> then it should be running ? smthg like "source(Rscript)"
>
> Hope you can help...
>
> Freddy
Consider a simple R script, hello_world.R like this:
print('Hello world');
print(commandArgs());
Then in Galaxy I think you'd need the default interpreter
("bash") and the command to be:
R --vanilla --file=hello_world.R --args "Args go here"
I'm assuming your script will write useful output to a
file, and stdout can be discarded.
However, what I originally had in mind was setting the
hash bang and executable bit with chmod so that you
can do this at the command line:
./hello_world.R "Args go here"
Once that works, calling it from Galaxy should be trivial.
I think one way to do this is with the little r package:
http://code.google.com/p/littler/
Peter
Hi Freddy,
I missed your earlier email about the r_wrapper.sh script
that comes with Galaxy, used like this where an R script
is created at run time from the XML wrapper using a
moderately complex Cheater template:
$ grep r_wrapper.sh tools/*/*.xml
tools/plotting/xy_plot.xml: <command interpreter="bash">r_wrapper.sh
$script_file</command>
tools/stats/lda_analy.xml: <command interpreter="sh">r_wrapper.sh
$script_file</command>
tools/stats/plot_from_lda.xml: <command interpreter="sh">r_wrapper.sh
$script_file</command>
In these examples only the script name is passed (all the
variable information is inside the dynamically generated
script file).
However, reading the shell script it *should* accept more than
one input, but the first input is interpreted as the script name.
Maybe that doesn't work since you said you tried it?
Clearly there are several ways to approach this (r_wrapper.sh,
rpy from python, etc). Guidance from the Galaxy developers on
what they consider to be best practice would be welcome.
Peter
10:40 a.m.
New subject: rpy or perl
Exactly,
That is what confused me.
Earlier I simply tried running it 'straight' and that didn't work so well.
Later I saw the wrappers thanks to James Taylor, but then it simply
didn't produce output.
so basically, I thought, I'm having a problem with in/output, so system
problems rahter than
R itself.
Thus, I was puzzled that galaxy itself was never using ANY R-script and
only rpy/xml.
But I will give R-straight another good try.
I've tried the things you mentioned, but I guess I have never used the
"--file=Rscript" option.
Will let you know how that goes.
Cheers,
Freddy
On 10/12/2010 12:28 PM, Peter wrote:
On Tue, Oct 12, 2010 at 11:15 AM,
Peter<peter(a)maubp.freeserve.co.uk> wrote:
> On Tue, Oct 12, 2010 at 10:43 AM, Freddy<freddy.debree(a)wur.nl> wrote:
>>
>> Hi Peter,
>>
>> Running R from xml is not so straight forward to me.
>> Is the interpreter "bash" or is it "R"?
>> If "bash"
>> then it should be running "R --vanilla --slave input<
Rscript>
>> output"
>> if "R"
>> then it should be running ? smthg like "source(Rscript)"
>>
>> Hope you can help...
>>
>> Freddy
> Consider a simple R script, hello_world.R like this:
>
> print('Hello world');
> print(commandArgs());
>
> Then in Galaxy I think you'd need the default interpreter
> ("bash") and the command to be:
>
> R --vanilla --file=hello_world.R --args "Args go here"
>
> I'm assuming your script will write useful output to a
> file, and stdout can be discarded.
>
> However, what I originally had in mind was setting the
> hash bang and executable bit with chmod so that you
> can do this at the command line:
>
> ./hello_world.R "Args go here"
>
> Once that works, calling it from Galaxy should be trivial.
> I think one way to do this is with the little r package:
> http://code.google.com/p/littler/
>
> Peter
>
Hi Freddy,
I missed your earlier email about the r_wrapper.sh script
that comes with Galaxy, used like this where an R script
is created at run time from the XML wrapper using a
moderately complex Cheater template:
$ grep r_wrapper.sh tools/*/*.xml
tools/plotting/xy_plot.xml:<command interpreter="bash">r_wrapper.sh
$script_file</command>
tools/stats/lda_analy.xml: <command interpreter="sh">r_wrapper.sh
$script_file</command>
tools/stats/plot_from_lda.xml: <command interpreter="sh">r_wrapper.sh
$script_file</command>
In these examples only the script name is passed (all the
variable information is inside the dynamically generated
script file).
However, reading the shell script it *should* accept more than
one input, but the first input is interpreted as the script name.
Maybe that doesn't work since you said you tried it?
Clearly there are several ways to approach this (r_wrapper.sh,
rpy from python, etc). Guidance from the Galaxy developers on
what they consider to be best practice would be welcome.
Peter
10:46 a.m.
New subject: rpy or perl
On Tue, Oct 12, 2010 at 11:40 AM, Freddy <freddy.debree(a)wur.nl> wrote:
Exactly,
That is what confused me.
Earlier I simply tried running it 'straight' and that didn't work so well.
Later I saw the wrappers thanks to James Taylor, but then it simply didn't
produce output.
so basically, I thought, I'm having a problem with in/output, so system
problems rahter than R itself.
Thus, I was puzzled that galaxy itself was never using ANY R-script and only
rpy/xml.
But I will give R-straight another good try.
I've tried the things you mentioned, but I guess I have never used the
"--file=Rscript" option.
Will let you know how that goes.
Cheers,
Freddy
As I understand it:
* Galaxy will capture stdout/stderr (unless you have redirected them),
stdout is discarded, and any text on stderr is treated as an error.
* If you want output from a script, it should be sent to a file
Since R tends to be very noisy on stdout, it is probably best to
ignore stdout and make any output explicit to a file (whose name
should be a command line argument which Galaxy will assign).
Please keep us posted - I do sometimes write plain R scripts myself,
although I have tended to use a Python script and rpy more often.
Peter
10:47 a.m.
New subject: rpy or perl
Just to note for those Perl people developing tools with Galaxy and
wanting to interface with R there are a couple of libraries out there
to do this for you:
RSPerl
http://www.omegahat.org/RSPerl/
Statistics::R
http://search.cpan.org/search?query=Statistics%3A%3AR
12:19 p.m.
New subject: rpy or perl
I am not using perl, but bash, which makes things much easier on the
cmd line.
However, maybe you know how to retrieve the R output or:
what exactly is the problem for Galaxy
for how to handle the system output from R through the shell?
We have seen it here with other tools as well.
R should work straight from the cmd line as well.
And everything - incl R - does when use bash in a shell, but as soon
as you put galaxy in between you and the program the output,
is nowhere to be seen
so far, we've been able to simply 'mv' the output from the program
towards bash and that will push it to galaxy.
But with R this didn't work. (so far)
On 10/13/2010 12:47 PM, Leandro Hermida wrote:
Just to note for those Perl people developing tools with Galaxy and
wanting to interface with R there are a couple of libraries out there
to do this for you:
RSPerl
http://www.omegahat.org/RSPerl/
Statistics::R
http://search.cpan.org/search?query=Statistics%3A%3AR
5:44 a.m.
New subject: rpy or perl
If I understand you correctly what you want to do you should be able to just do that by a
tool.xml config calling an R script and providing a data file. The R script can open that
file and process it into some output file known by galaxy.... But maybe I oversee
something.
In your tool_config grab an R-file and some datafile:
<command>
R --slave -f $in_r --args $in_data $out_data
</command>
<inputs>
<param name="in_data" type="data" format="tabular"
label="Test data file" />
<param name="in_r" type="data" format="text"
label="R script to load and execute" />
</inputs>
<outputs>
<data name="out_data" type="data" format="tabular"
label="R script output" />
</outputs>
The R script provided will grab the args from the cmd line as you indiciated earlier:
# R script file to grab input and output filenames from cmdline and just copy
args <- commandArgs()
output <- read.table(args[6], header=T)
write.table(output,sep="\t",file=args[7],row.names=F)
#end script
Hope this helped,
Alex
________________________________________
Van: galaxy-dev-bounces(a)lists.bx.psu.edu [galaxy-dev-bounces(a)lists.bx.psu.edu] namens
Freddy [freddy.debree(a)wur.nl]
Verzonden: woensdag 13 oktober 2010 14:19
Aan: galaxy-dev(a)lists.bx.psu.edu
Onderwerp: Re: [galaxy-dev] rpy or perl
I am not using perl, but bash, which makes things much easier on the
cmd line.
However, maybe you know how to retrieve the R output or:
what exactly is the problem for Galaxy
for how to handle the system output from R through the shell?
We have seen it here with other tools as well.
R should work straight from the cmd line as well.
And everything - incl R - does when use bash in a shell, but as soon
as you put galaxy in between you and the program the output,
is nowhere to be seen
so far, we've been able to simply 'mv' the output from the program
towards bash and that will push it to galaxy.
But with R this didn't work. (so far)
On 10/13/2010 12:47 PM, Leandro Hermida wrote:
Just to note for those Perl people developing tools with Galaxy and
wanting to interface with R there are a couple of libraries out there
to do this for you:
RSPerl
http://www.omegahat.org/RSPerl/
Statistics::R
http://search.cpan.org/search?query=Statistics%3A%3AR
_______________________________________________
galaxy-dev mailing list
galaxy-dev(a)lists.bx.psu.edu
http://lists.bx.psu.edu/listinfo/galaxy-dev
9:45 a.m.
New subject: rpy or perl
On Thu, Oct 14, 2010 at 6:44 AM, Bossers, Alex <Alex.Bossers(a)wur.nl> wrote:
If I understand you correctly what you want to do you should be able to just
do that by a tool.xml config calling an R script and providing a data file. The
R script can open that file and process it into some output file known by
galaxy.... But maybe I oversee something.
In your tool_config grab an R-file and some datafile:
<command>
R --slave -f $in_r --args $in_data $out_data
</command>
<inputs>
<param name="in_data" type="data" format="tabular"
label="Test data file" />
<param name="in_r" type="data" format="text"
label="R script to load and execute" />
</inputs>
<outputs>
<data name="out_data" type="data" format="tabular"
label="R script output" />
</outputs>
The R script provided will grab the args from the cmd line as you indiciated earlier:
# R script file to grab input and output filenames from cmdline and just copy
args <- commandArgs()
output <- read.table(args[6], header=T)
write.table(output,sep="\t",file=args[7],row.names=F)
#end script
Hope this helped,
Alex
Wow - very similar to the version I wrote (off list discussion yesterday).
You can also try something like this if the script writes to stdout:
<command>
R --slave -f $in_r --args $in_data > $out_data
</command>
Peter
5 p.m.
New subject: Error when transfer sample
Hi,
I have made a lot of progress getting the LIMS system up and running and not I'm at
the point where I was able to connect to the folders having my sequence data from galaxy.
I can select a sample from a list of submitted samples in the tracking form and then match
it to a file in our sequence directory.
I get an error when trying to transfer the sample to galaxy.
Does anybody have any ideas where should I start looking to fix this?
Error below.
Thanks in advance.
Victor
Last couple of lines are,
NoSectionError: No section: 'data_transfer_user_login_info'
On Oct 14, 2010, at 12:44 AM, Bossers, Alex wrote:
If I understand you correctly what you want to do you should be able
to just do that by a tool.xml config calling an R script and providing a data file. The R
script can open that file and process it into some output file known by galaxy.... But
maybe I oversee something.
In your tool_config grab an R-file and some datafile:
<command>
R --slave -f $in_r --args $in_data $out_data
</command>
<inputs>
<param name="in_data" type="data" format="tabular"
label="Test data file" />
<param name="in_r" type="data" format="text"
label="R script to load and execute" />
</inputs>
<outputs>
<data name="out_data" type="data" format="tabular"
label="R script output" />
</outputs>
The R script provided will grab the args from the cmd line as you indiciated earlier:
# R script file to grab input and output filenames from cmdline and just copy
args <- commandArgs()
output <- read.table(args[6], header=T)
write.table(output,sep="\t",file=args[7],row.names=F)
#end script
Hope this helped,
Alex
________________________________________
Van: galaxy-dev-bounces(a)lists.bx.psu.edu [galaxy-dev-bounces(a)lists.bx.psu.edu] namens
Freddy [freddy.debree(a)wur.nl]
Verzonden: woensdag 13 oktober 2010 14:19
Aan: galaxy-dev(a)lists.bx.psu.edu
Onderwerp: Re: [galaxy-dev] rpy or perl
I am not using perl, but bash, which makes things much easier on the
cmd line.
However, maybe you know how to retrieve the R output or:
what exactly is the problem for Galaxy
for how to handle the system output from R through the shell?
We have seen it here with other tools as well.
R should work straight from the cmd line as well.
And everything - incl R - does when use bash in a shell, but as soon
as you put galaxy in between you and the program the output,
is nowhere to be seen
so far, we've been able to simply 'mv' the output from the program
towards bash and that will push it to galaxy.
But with R this didn't work. (so far)
On 10/13/2010 12:47 PM, Leandro Hermida wrote:
> Just to note for those Perl people developing tools with Galaxy and
> wanting to interface with R there are a couple of libraries out there
> to do this for you:
>
> RSPerl
> http://www.omegahat.org/RSPerl/
>
> Statistics::R
> http://search.cpan.org/search?query=Statistics%3A%3AR
>
_______________________________________________
galaxy-dev mailing list
galaxy-dev(a)lists.bx.psu.edu
http://lists.bx.psu.edu/listinfo/galaxy-dev
_______________________________________________
galaxy-dev mailing list
galaxy-dev(a)lists.bx.psu.edu
http://lists.bx.psu.edu/listinfo/galaxy-dev
Error Traceback:
View as: Interactive | Text | XML (full)
⇝ NoSectionError: No section: 'data_transfer_user_login_info'
URL:
http://mir-13:8087/requests_admin/manage_datasets?sort=-create_time&o...
Module weberror.evalexception.middleware:364 in respond view
> app_iter = self.application(environ, detect_start_response)
Module paste.debug.prints:98 in __call__ view
> environ, self.app)
Module paste.wsgilib:539 in
intercept_output view
> app_iter = application(environ, replacement_start_response)
Module paste.recursive:80 in __call__ view
> return self.application(environ, start_response)
Module
paste.httpexceptions:632 in __call__ view
> return self.application(environ, start_response)
Module
galaxy.web.framework.base:145 in __call__ view
> body = method( trans, **kwargs )
Module
galaxy.web.framework:139 in decorator view
> return func( self, trans, *args, **kwargs )
Module
galaxy.web.controllers.requests_admin:469 in manage_datasets view
> self.__start_datatx(trans, sample_dataset.sample, id_list)
Module galaxy.web.controllers.requests_admin:837 in __start_datatx view
> datatx_user = self.__setup_datatx_user(trans, sample.library,
sample.folder)
Module galaxy.web.controllers.requests_admin:739 in
__setup_datatx_user view
> email = config.get("data_transfer_user_login_info",
"email")
Module ConfigParser:511 in get view
<< except KeyError:
if section != DEFAULTSECT:
raise NoSectionError(section)
# Update with the entry specific variables
if vars:
NoSectionError: No section: 'data_transfer_user_login_info'
5:21 p.m.
New subject: Error when transfer sample
Victor,
You will need to setup data transfer in sample tracking before you
start using it. This page (http://main.g2.bx.psu.edu/u/rkchak/p/sts-setup-data-transfer
) describes it step by step.
Let me know if you have more questions.
thanks
rc
On Oct 14, 2010, at 1:00 PM, Victor Ruotti wrote:
Hi,
I have made a lot of progress getting the LIMS system up and running
and not I'm at the point where I was able to connect to the folders
having my sequence data from galaxy.
I can select a sample from a list of submitted samples in the
tracking form and then match it to a file in our sequence directory.
I get an error when trying to transfer the sample to galaxy.
Does anybody have any ideas where should I start looking to fix this?
Error below.
Thanks in advance.
Victor
Last couple of lines are,
NoSectionError: No section: 'data_transfer_user_login_info'
On Oct 14, 2010, at 12:44 AM, Bossers, Alex wrote:
> If I understand you correctly what you want to do you should be
> able to just do that by a tool.xml config calling an R script and
> providing a data file. The R script can open that file and process
> it into some output file known by galaxy.... But maybe I oversee
> something.
>
> In your tool_config grab an R-file and some datafile:
>
> <command>
> R --slave -f $in_r --args $in_data $out_data
> </command>
> <inputs>
> <param name="in_data" type="data"
format="tabular"
> label="Test data file" />
> <param name="in_r" type="data" format="text"
label="R script
> to load and execute" />
> </inputs>
> <outputs>
> <data name="out_data" type="data"
format="tabular" label="R
> script output" />
> </outputs>
>
>
> The R script provided will grab the args from the cmd line as you
> indiciated earlier:
>
> # R script file to grab input and output filenames from cmdline
> and just copy
> args <- commandArgs()
> output <- read.table(args[6], header=T)
> write.table(output,sep="\t",file=args[7],row.names=F)
> #end script
>
>
> Hope this helped,
>
> Alex
>
>
>
> ________________________________________
> Van: galaxy-dev-bounces(a)lists.bx.psu.edu [galaxy-dev-bounces(a)lists.bx.psu.edu
> ] namens Freddy [freddy.debree(a)wur.nl]
> Verzonden: woensdag 13 oktober 2010 14:19
> Aan: galaxy-dev(a)lists.bx.psu.edu
> Onderwerp: Re: [galaxy-dev] rpy or perl
>
> I am not using perl, but bash, which makes things much easier on the
> cmd line.
> However, maybe you know how to retrieve the R output or:
> what exactly is the problem for Galaxy
> for how to handle the system output from R through the shell?
> We have seen it here with other tools as well.
> R should work straight from the cmd line as well.
> And everything - incl R - does when use bash in a shell, but as soon
> as you put galaxy in between you and the program the output,
> is nowhere to be seen
>
> so far, we've been able to simply 'mv' the output from the program
> towards bash and that will push it to galaxy.
> But with R this didn't work. (so far)
>
> On 10/13/2010 12:47 PM, Leandro Hermida wrote:
>> Just to note for those Perl people developing tools with Galaxy and
>> wanting to interface with R there are a couple of libraries out
>> there
>> to do this for you:
>>
>> RSPerl
>> http://www.omegahat.org/RSPerl/
>>
>> Statistics::R
>> http://search.cpan.org/search?query=Statistics%3A%3AR
>>
>
> _______________________________________________
> galaxy-dev mailing list
> galaxy-dev(a)lists.bx.psu.edu
> http://lists.bx.psu.edu/listinfo/galaxy-dev
>
> _______________________________________________
> galaxy-dev mailing list
> galaxy-dev(a)lists.bx.psu.edu
> http://lists.bx.psu.edu/listinfo/galaxy-dev
Error Traceback:
View as: Interactive | Text | XML (full)
⇝ NoSectionError: No section: 'data_transfer_user_login_info'
URL: http://mir-13:8087/requests_admin/manage_datasets?sort=-
create_time&operation=Start+Transfer&id=df7a1f0c02a5b08e
Module weberror.evalexception.middleware:364 in respond
<plus.jpg> view
>> app_iter = self.application(environ, detect_start_response)
Module paste.debug.prints:98 in __call__ <plus.jpg> view
>> environ, self.app)
Module paste.wsgilib:539 in intercept_output <plus.jpg> view
>> app_iter = application(environ, replacement_start_response)
Module paste.recursive:80 in __call__ <plus.jpg> view
>> return self.application(environ, start_response)
Module paste.httpexceptions:632 in __call__ <plus.jpg> view
>> return self.application(environ, start_response)
Module galaxy.web.framework.base:145 in __call__ <plus.jpg>
view
>> body = method( trans, **kwargs )
Module galaxy.web.framework:139 in decorator <plus.jpg> view
>> return func( self, trans, *args, **kwargs )
Module galaxy.web.controllers.requests_admin:469 in
manage_datasets <plus.jpg> view
>> self.__start_datatx(trans, sample_dataset.sample, id_list)
Module galaxy.web.controllers.requests_admin:837 in
__start_datatx <plus.jpg> view
>> datatx_user = self.__setup_datatx_user(trans, sample.library,
sample.folder)
Module galaxy.web.controllers.requests_admin:739 in
__setup_datatx_user <plus.jpg> view
>> email = config.get("data_transfer_user_login_info",
"email")
Module ConfigParser:511 in get <plus.jpg> view
<< except KeyError:
if section != DEFAULTSECT:
raise NoSectionError(section)
# Update with the entry specific variables
if vars:
NoSectionError: No section: 'data_transfer_user_login_info'
_______________________________________________
galaxy-dev mailing list
galaxy-dev(a)lists.bx.psu.edu
http://lists.bx.psu.edu/listinfo/galaxy-dev
4491
days inactive
4493
days old
galaxy-dev@lists.galaxyproject.org
9 comments
6 participants
participants (6)
-
Bossers, Alex -
Freddy -
Leandro Hermida -
Peter -
Ramkrishna Chakrabarty -
Victor Ruotti