can not open perl script: Permission denied

[rolan]

I have recently installed perl and circos in windows - Im completely new to both. So, excuse my questions if there are so obvious to resolve ...I have had some issues with config-general

and GD but it appears I have those resolved.  Now, Im running into trouble with opening perl scripts.

the path that I have is Perl\circos\bin\circos...So, Im not really sure how to execute the script.

I have done various things...One of those things I have tried is: 

C:\Perl> perl circos -conf\bin\circos.conf 

and I get the following error message:  can not open perl script "circos": Permission denied

My perl -V checks well...so, I guess perl is running fine....

Thanks in advance,

rolan.

[Paulo Nuin]

On 2013-03-13, at 9:25 PM, rolan <genomi...@gmail.com> wrote:

I have recently installed perl and circos in windows - Im completely new to both. So, excuse my questions if there are so obvious to resolve ...I have had some issues with config-general

and GD but it appears I have those resolved.  Now, Im running into trouble with opening perl scripts.

the path that I have is Perl\circos\bin\circos...So, Im not really sure how to execute the script.

I have done various things...One of those things I have tried is: 

C:\Perl> perl circos -conf\bin\circos.conf 

Do you have a space between -conf and \bin\…?

and I get the following error message:  can not open perl script "circos": Permission denied

My perl -V checks well...so, I guess perl is running fine....

Thanks in advance,

rolan.

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[rolan]

Nuin,

I just put a space between conf and bin and did the same thing...

rolan

[Paulo Nuin]

So, you are running circos from a wrong directory. It seems that you have perl at c:\perl and where to you have circos? Let's say circos is on c:\circos you would have to have to do this to run properly from C:\>

C:\> cd circos

C:\circos> cd bin

C:\circos\bin> C:\Perl\perl.exe circos -conf <path to circos configuration file>

Cheers

Paulo

--

[rolan]

Hello Paulo,

I have circos inside the Perl folder (C: \> Perl\circos).  I will try it from outside from Perl folder...

Thanks,

rolan.

On Thursday, March 14, 2013 8:58:28 AM UTC-5, nuin wrote:

So, you are running circos from a wrong directory. It seems that you have perl at c:\perl and where to you have circos? Let's say circos is on c:\circos you would have to have to do this to run properly from C:\>

C:\> cd circos

C:\circos> cd bin

C:\circos\bin> C:\Perl\perl.exe circos -conf <path to circos configuration file>

Cheers

Paulo

On Thu, Mar 14, 2013 at 9:19 AM, rolan <genomi...@gmail.com> wrote:

Nuin,

I just put a space between conf and bin and did the same thing...

rolan

On Wednesday, March 13, 2013 8:25:19 PM UTC-5, rolan wrote:

I have recently installed perl and circos in windows - Im completely new to both. So, excuse my questions if there are so obvious to resolve ...I have had some issues with config-general

and GD but it appears I have those resolved.  Now, Im running into trouble with opening perl scripts.

the path that I have is Perl\circos\bin\circos...So, Im not really sure how to execute the script.

I have done various things...One of those things I have tried is: 

C:\Perl> perl circos -conf\bin\circos.conf 

and I get the following error message:  can not open perl script "circos": Permission denied

My perl -V checks well...so, I guess perl is running fine....

Thanks in advance,

rolan.

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[rolan]

Paulo,

I have enter: 

C:\circos\bin> perl circos -conf \ circos\bin\circos.conf <path to configuration file>

and got :configuration file error

I just wrote down perl which calls explicitly for perl, follow by the file and then path to configuration file.

Thanks...

On Thursday, March 14, 2013 8:58:28 AM UTC-5, nuin wrote:

So, you are running circos from a wrong directory. It seems that you have perl at c:\perl and where to you have circos? Let's say circos is on c:\circos you would have to have to do this to run properly from C:\>

C:\> cd circos

C:\circos> cd bin

C:\circos\bin> C:\Perl\perl.exe circos -conf <path to circos configuration file>

Cheers

Paulo

On Thu, Mar 14, 2013 at 9:19 AM, rolan <genomi...@gmail.com> wrote:

Nuin,

I just put a space between conf and bin and did the same thing...

rolan

On Wednesday, March 13, 2013 8:25:19 PM UTC-5, rolan wrote:

I have recently installed perl and circos in windows - Im completely new to both. So, excuse my questions if there are so obvious to resolve ...I have had some issues with config-general

and GD but it appears I have those resolved.  Now, Im running into trouble with opening perl scripts.

the path that I have is Perl\circos\bin\circos...So, Im not really sure how to execute the script.

I have done various things...One of those things I have tried is: 

C:\Perl> perl circos -conf\bin\circos.conf 

and I get the following error message:  can not open perl script "circos": Permission denied

My perl -V checks well...so, I guess perl is running fine....

Thanks in advance,

rolan.

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[rolan]

Paulo,

Do I have a config installation issue? see config-General post

Thanks in advance...

I can not read perl scripts on windows....errror: the config-General file seems to be missing. I do have installed the file (I have checked with PPM in strawberry and is up to date)... On my directory, it is under perl(strawberry)\myperl(required mod

Mar 13 (15 hours ago)  Martin It looks like your Perl may not be seeing this module. Are you sure it is correctly installed? Does this work, or produce an error: perl -MConfig::General Martin Krzywinskiscience + arthttp://mkweb.bcgsc.ca

me (rolan change)

Mar 13 (14 hours ago)

Hi Martin,

No...It did not do anything (no error) or c:\prompt.....So, I take it is not installed properly??

Any advise on how to properly install it.

Thanks in advance,

[rolan]

Do I have a configuration issue?? (see config-General issue post)

Thanks,

rolan.

[Paulo Nuin]

Hi

It doesn't matter where you have installed, as long as you point to the right location. If circos is on C:\Perl\circosXYZ just run like this

cd Perl\circosXYZ

C:\Perl\perl.exe bin\circos -conf <path to configuration>

Cheers

Paulo

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[Martin Krzywinski]

If the command

perl -MConfig::General

does not produce an outright error, then the module is installed correctly. 

> C:\circos\bin> perl circos -conf \ circos\bin\circos.conf <path to configuration file>

It looks like you're new to the command line. Please read these tutorial

http://www.circos.ca/documentation/tutorials/configuration/unix_vs_windows/

http://www.cs.princeton.edu/courses/archive/spr05/cos126/cmd-prompt.html

which explains in detail how to run Circos and the purpose of the command-line switches.

Where Paolo wrote <path to configuration file>, you are meant to replace this string with the actual path to your configuration file.

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

[rolan]

got it now....

C:\circos\bin>perl circos -conf \tutorials\2\2\circos.conf

Thanks,

rolan.

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