Thread: [Useq-users] R environment

Brought to you by: biotelerock, bmilash, elainegee, scourdy, tmosbruger

useq-users

[Useq-users] R environment

From: Radhouane A. <ar...@gm...> - 2011-10-18 14:18:32

Hello everyone,

Is there any option with USeq where we can specify the location of R
binaries, I am working on a server on which I have no permission to change
R, so I installed R-2.13.0 in a different folder made my setenv changes but
I have an error message saying :

Cannot find or execute the R application -> /usr/bin/R

Any help ?

Thanks

Radhouane

Re: [Useq-users] R environment

From: David N. <dav...@gm...> - 2011-10-18 14:23:02

Hello Radhouane,

I believe each of the apps that use R have a r option that lets you specify
where R is?  Which app were you trying to run? Did you take a look at the
command line options (launch the app with no arguments).  -cheers, D



From:  Radhouane Aniba <ar...@gm...>
Date:  Tue, 18 Oct 2011 10:18:06 -0400
To:  <use...@li...>
Subject:  [Useq-users] R environment

Hello everyone,

Is there any option with USeq where we can specify the location of R
binaries, I am working on a server on which I have no permission to change
R, so I installed R-2.13.0 in a different folder made my setenv changes but
I have an error message saying :

Cannot find or execute the R application -> /usr/bin/R

Any help ?

Thanks

Radhouane


----------------------------------------------------------------------------
-- All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security threats,
fraudulent activity and more. Splunk takes this data and makes sense of it.
Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2d-oct__________________________________________
_____ Useq-users mailing list Use...@li...
https://lists.sourceforge.net/lists/listinfo/useq-users

Re: [Useq-users] R environment

From: Radhouane A. <ar...@gm...> - 2011-10-18 14:24:40

I am using the Chip-seq app will take a look at its options.

Radhouane

2011/10/18 David Nix <dav...@gm...>

> Hello Radhouane,
>
> I believe each of the apps that use R have a –r option that lets you
> specify where R is?  Which app were you trying to run? Did you take a look
> at the command line options (launch the app with no arguments).  -cheers, D
>
>
>
> From: Radhouane Aniba <ar...@gm...>
> Date: Tue, 18 Oct 2011 10:18:06 -0400
> To: <use...@li...>
> Subject: [Useq-users] R environment
>
> Hello everyone,
>
> Is there any option with USeq where we can specify the location of R
> binaries, I am working on a server on which I have no permission to change
> R, so I installed R-2.13.0 in a different folder made my setenv changes but
> I have an error message saying :
>
> Cannot find or execute the R application -> /usr/bin/R
>
> Any help ?
>
> Thanks
>
> Radhouane
>
>
> ------------------------------------------------------------------------------
> All the data continuously generated in your IT infrastructure contains a
> definitive record of customers, application performance, security threats,
> fraudulent activity and more. Splunk takes this data and makes sense of it.
> Business sense. IT sense. Common sense.
> http://p.sf.net/sfu/splunk-d2d-oct_______________________________________________Useq-users mailing list
> Use...@li...
> https://lists.sourceforge.net/lists/listinfo/useq-users
>



-- 
*Radhouane Aniba*
*Bioinformatics Postdoctoral Research Scientist*
*Institute for Advanced Computer Studies
Center for Bioinformatics and Computational Biology* *(CBCB)*
*University of Maryland, College Park
MD 20742*

Re: [Useq-users] R environment

From: Radhouane A. <ar...@gm...> - 2011-10-18 14:44:13

Thank you David,

It works but generated a bug I dont understand it, sorry I am just starting
using it :

Parsing PointData from raw alignments...
    Parsing treatment PointData...
    /fs/sh-data/USeq/Data/DNAse/RESULTS/PointData/TreatmentPointData/Rep0
java.lang.ArrayIndexOutOfBoundsException: 5
    at
edu.utah.seq.parsers.Tag2Point.splitBedFilesToTemp(Tag2Point.java:206)
    at edu.utah.seq.parsers.Tag2Point.<init>(Tag2Point.java:76)
    at edu.utah.seq.analysis.ChIPSeq.parsePointData(ChIPSeq.java:306)
    at edu.utah.seq.analysis.ChIPSeq.parsePointData(ChIPSeq.java:236)
    at edu.utah.seq.analysis.ChIPSeq.<init>(ChIPSeq.java:73)
    at edu.utah.seq.analysis.ChIPSeq.main(ChIPSeq.java:449)

My Input files are in this format :

chr1    161    181        250    +
chr1    164    184        250    +
chr1    237    257        333    +

Thanks

Radhouane



2011/10/18 Radhouane Aniba <ar...@gm...>

> I am using the Chip-seq app will take a look at its options.
>
> Radhouane
>
>
> 2011/10/18 David Nix <dav...@gm...>
>
>> Hello Radhouane,
>>
>> I believe each of the apps that use R have a –r option that lets you
>> specify where R is?  Which app were you trying to run? Did you take a look
>> at the command line options (launch the app with no arguments).  -cheers, D
>>
>>
>>
>> From: Radhouane Aniba <ar...@gm...>
>> Date: Tue, 18 Oct 2011 10:18:06 -0400
>> To: <use...@li...>
>> Subject: [Useq-users] R environment
>>
>> Hello everyone,
>>
>> Is there any option with USeq where we can specify the location of R
>> binaries, I am working on a server on which I have no permission to change
>> R, so I installed R-2.13.0 in a different folder made my setenv changes but
>> I have an error message saying :
>>
>> Cannot find or execute the R application -> /usr/bin/R
>>
>> Any help ?
>>
>> Thanks
>>
>> Radhouane
>>
>>
>> ------------------------------------------------------------------------------
>> All the data continuously generated in your IT infrastructure contains a
>> definitive record of customers, application performance, security threats,
>> fraudulent activity and more. Splunk takes this data and makes sense of it.
>> Business sense. IT sense. Common sense.
>> http://p.sf.net/sfu/splunk-d2d-oct_______________________________________________Useq-users mailing list
>> Use...@li...
>> https://lists.sourceforge.net/lists/listinfo/useq-users
>>
>
>
>
> --
> *Radhouane Aniba*
> *Bioinformatics Postdoctoral Research Scientist*
> *Institute for Advanced Computer Studies
> Center for Bioinformatics and Computational Biology* *(CBCB)*
> *University of Maryland, College Park
> MD 20742*
>
>


-- 
*Radhouane Aniba*
*Bioinformatics Postdoctoral Research Scientist*
*Institute for Advanced Computer Studies
Center for Bioinformatics and Computational Biology* *(CBCB)*
*University of Maryland, College Park
MD 20742*

Re: [Useq-users] R environment

From: David N. <dav...@gm...> - 2011-10-18 15:38:33

Could you send your command-line as well as a txt file containing a bit of
the input files (head input.txt > subInput.txt or gunzip c input.txt.gz |
head > subInput.txt if gzipped)?  I suspect the Tag2Point app is parsing on
white space and your number of columns is getting collapsed so that the
strand column is actually one less.

-cheers, David

From:  Radhouane Aniba <ar...@gm...>
Date:  Tue, 18 Oct 2011 10:41:55 -0400
To:  David Nix <dav...@gm...>
Cc:  <use...@li...>
Subject:  Re: [Useq-users] R environment

Thank you David,

It works but generated a bug I dont understand it, sorry I am just starting
using it :

Parsing PointData from raw alignments...
    Parsing treatment PointData...
    /fs/sh-data/USeq/Data/DNAse/RESULTS/PointData/TreatmentPointData/Rep0
java.lang.ArrayIndexOutOfBoundsException: 5
    at 
edu.utah.seq.parsers.Tag2Point.splitBedFilesToTemp(Tag2Point.java:206)
    at edu.utah.seq.parsers.Tag2Point.<init>(Tag2Point.java:76)
    at edu.utah.seq.analysis.ChIPSeq.parsePointData(ChIPSeq.java:306)
    at edu.utah.seq.analysis.ChIPSeq.parsePointData(ChIPSeq.java:236)
    at edu.utah.seq.analysis.ChIPSeq.<init>(ChIPSeq.java:73)
    at edu.utah.seq.analysis.ChIPSeq.main(ChIPSeq.java:449)

My Input files are in this format :

chr1    161    181        250    +
chr1    164    184        250    +
chr1    237    257        333    +

Thanks

Radhouane



2011/10/18 Radhouane Aniba <ar...@gm...>
> I am using the Chip-seq app will take a look at its options.
> 
> Radhouane
> 
> 
> 2011/10/18 David Nix <dav...@gm...>
>> Hello Radhouane,
>> 
>> I believe each of the apps that use R have a r option that lets you specify
>> where R is?  Which app were you trying to run? Did you take a look at the
>> command line options (launch the app with no arguments).  -cheers, D
>> 
>> 
>> 
>> From:  Radhouane Aniba <ar...@gm...>
>> Date:  Tue, 18 Oct 2011 10:18:06 -0400
>> To:  <use...@li...>
>> Subject:  [Useq-users] R environment
>> 
>> Hello everyone,
>> 
>> Is there any option with USeq where we can specify the location of R
>> binaries, I am working on a server on which I have no permission to change R,
>> so I installed R-2.13.0 in a different folder made my setenv changes but I
>> have an error message saying :
>> 
>> Cannot find or execute the R application -> /usr/bin/R
>> 
>> Any help ?
>> 
>> Thanks
>> 
>> Radhouane
>> 
>> 
>> -----------------------------------------------------------------------------
>> - All the data continuously generated in your IT infrastructure contains a
>> definitive record of customers, application performance, security threats,
>> fraudulent activity and more. Splunk takes this data and makes sense of it.
>> Business sense. IT sense. Common sense.
>> http://p.sf.net/sfu/splunk-d2d-oct___________________________________________
>> ____ Useq-users mailing list
>> Use...@li...https://lists.sourceforge.net/lists/listinfo/
>> useq-users
> 
> 
> 
> -- 
> Radhouane Aniba
> Bioinformatics Postdoctoral Research Scientist
> Institute for Advanced Computer Studies
> Center for Bioinformatics and Computational Biology (CBCB)
> University of Maryland, College Park
> MD 20742
> 



-- 
Radhouane Aniba
Bioinformatics Postdoctoral Research Scientist
Institute for Advanced Computer Studies
Center for Bioinformatics and Computational Biology (CBCB)
University of Maryland, College Park
MD 20742