running my first pipeline

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running my first pipeline

kmuthuraman
Hello
I just installed ergatis and workflow manager.

I'm not having much luck in building a simple pipeline with existing
components. I followed the steps in
ergatis/cgi/documentation.cgi?article=pipeline_creation, but I don't see
the pipeline running.

I just added the formatDB component on a fasta file. I included the
$;FORMATDB_EXEC$; mentioned in /apps/ergatis/docs/formatdb.xml in
/apps/ergatis/software.config and provided the full path to the fasta
file in the interface.

When I clicked on "Run Pipeline", the component seems to run forever.
The fasta file is really small and the run should not take more than a
few seconds.

When I click on "view log" I get " : "pass file at
/var/www/html/ergatis/cgi/view_formatted_log_source.cgi line 14.".
It is expecting a file to be created under workflow/runtime which is not
being created.

Any suggestions ?

Thanks for your time. I appreciate your help.



Sincerely,
Karthik Narayan



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Re: running my first pipeline

Jason Kwan
Hi Karthik,

I have a vague recollection of running into a similar error message.  It
seems to be at a point in the cgi script where it is trying to write to
the scratch/tmp workflow space (although the devs should correct me if I
am wrong).  I would check through /<web documents
directory>/ergatis/cgi/ergatis.ini, and set all the tmp dirs and
everything (I'm thinking it could be to do with the temp_space and
workflow_run_dir variables, but you should check the others too).  The
important thing is that wherever you choose to put these directories,
make sure 1. they exist and 2. they have read/write permissions for
every user (i.e. chmod a+rw).  The ergatis pipelines are run by a
special apache user, rather than whatever your username is on the server.

Jason

On 6/13/11 3:43 PM, Muthuraman, Karthik Narayan (K) wrote:

> Hello
> I just installed ergatis and workflow manager.
>
> I'm not having much luck in building a simple pipeline with existing
> components. I followed the steps in
> ergatis/cgi/documentation.cgi?article=pipeline_creation, but I don't see
> the pipeline running.
>
> I just added the formatDB component on a fasta file. I included the
> $;FORMATDB_EXEC$; mentioned in /apps/ergatis/docs/formatdb.xml in
> /apps/ergatis/software.config and provided the full path to the fasta
> file in the interface.
>
> When I clicked on "Run Pipeline", the component seems to run forever.
> The fasta file is really small and the run should not take more than a
> few seconds.
>
> When I click on "view log" I get " : "pass file at
> /var/www/html/ergatis/cgi/view_formatted_log_source.cgi line 14.".
> It is expecting a file to be created under workflow/runtime which is not
> being created.
>
> Any suggestions ?
>
> Thanks for your time. I appreciate your help.
>
>
>
> Sincerely,
> Karthik Narayan
>
>
>
> ------------------------------------------------------------------------------
> EditLive Enterprise is the world's most technically advanced content
> authoring tool. Experience the power of Track Changes, Inline Image
> Editing and ensure content is compliant with Accessibility Checking.
> http://p.sf.net/sfu/ephox-dev2dev
> _______________________________________________
> Ergatis-users mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/ergatis-users


------------------------------------------------------------------------------
EditLive Enterprise is the world's most technically advanced content
authoring tool. Experience the power of Track Changes, Inline Image
Editing and ensure content is compliant with Accessibility Checking.
http://p.sf.net/sfu/ephox-dev2dev
_______________________________________________
Ergatis-users mailing list
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Re: running my first pipeline

Joshua Orvis
Karthik -

If the log file isn't even being created it looks like Workflow is failing to be invoked.  Did you try running the "check_installation.pl" script that's found in your install tarball?  You pass it your INI file and it attempts to check and make sure your directory permissions, etc. are set correctly.  That's the first starting point.

Joshua



On Mon, Jun 13, 2011 at 6:47 PM, Jason Kwan <[hidden email]> wrote:
Hi Karthik,

I have a vague recollection of running into a similar error message.  It
seems to be at a point in the cgi script where it is trying to write to
the scratch/tmp workflow space (although the devs should correct me if I
am wrong).  I would check through /<web documents
directory>/ergatis/cgi/ergatis.ini, and set all the tmp dirs and
everything (I'm thinking it could be to do with the temp_space and
workflow_run_dir variables, but you should check the others too).  The
important thing is that wherever you choose to put these directories,
make sure 1. they exist and 2. they have read/write permissions for
every user (i.e. chmod a+rw).  The ergatis pipelines are run by a
special apache user, rather than whatever your username is on the server.

Jason

On 6/13/11 3:43 PM, Muthuraman, Karthik Narayan (K) wrote:
> Hello
> I just installed ergatis and workflow manager.
>
> I'm not having much luck in building a simple pipeline with existing
> components. I followed the steps in
> ergatis/cgi/documentation.cgi?article=pipeline_creation, but I don't see
> the pipeline running.
>
> I just added the formatDB component on a fasta file. I included the
> $;FORMATDB_EXEC$; mentioned in /apps/ergatis/docs/formatdb.xml in
> /apps/ergatis/software.config and provided the full path to the fasta
> file in the interface.
>
> When I clicked on "Run Pipeline", the component seems to run forever.
> The fasta file is really small and the run should not take more than a
> few seconds.
>
> When I click on "view log" I get " : "pass file at
> /var/www/html/ergatis/cgi/view_formatted_log_source.cgi line 14.".
> It is expecting a file to be created under workflow/runtime which is not
> being created.
>
> Any suggestions ?
>
> Thanks for your time. I appreciate your help.
>
>
>
> Sincerely,
> Karthik Narayan
>
>
>
> ------------------------------------------------------------------------------
> EditLive Enterprise is the world's most technically advanced content
> authoring tool. Experience the power of Track Changes, Inline Image
> Editing and ensure content is compliant with Accessibility Checking.
> http://p.sf.net/sfu/ephox-dev2dev
> _______________________________________________
> Ergatis-users mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/ergatis-users


------------------------------------------------------------------------------
EditLive Enterprise is the world's most technically advanced content
authoring tool. Experience the power of Track Changes, Inline Image
Editing and ensure content is compliant with Accessibility Checking.
http://p.sf.net/sfu/ephox-dev2dev
_______________________________________________
Ergatis-users mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/ergatis-users


------------------------------------------------------------------------------
EditLive Enterprise is the world's most technically advanced content
authoring tool. Experience the power of Track Changes, Inline Image
Editing and ensure content is compliant with Accessibility Checking.
http://p.sf.net/sfu/ephox-dev2dev
_______________________________________________
Ergatis-users mailing list
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Re: running my first pipeline

kmuthuraman

Thank you Joshua. I did try the ./check_installation script. It produced some warnings and error messages, but resulted in “PASS”.

 

Sincerely,
Karthik Narayan

 

From: Joshua Orvis [mailto:[hidden email]]
Sent: Tuesday, June 14, 2011 10:46 AM
To: [hidden email]; [hidden email]; Muthuraman, Karthik Narayan (K)
Subject: Re: [Ergatis-users] running my first pipeline

 

Karthik -

If the log file isn't even being created it looks like Workflow is failing to be invoked.  Did you try running the "check_installation.pl" script that's found in your install tarball?  You pass it your INI file and it attempts to check and make sure your directory permissions, etc. are set correctly.  That's the first starting point.

Joshua


On Mon, Jun 13, 2011 at 6:47 PM, Jason Kwan <[hidden email]> wrote:

Hi Karthik,

I have a vague recollection of running into a similar error message.  It
seems to be at a point in the cgi script where it is trying to write to
the scratch/tmp workflow space (although the devs should correct me if I
am wrong).  I would check through /<web documents
directory>/ergatis/cgi/ergatis.ini, and set all the tmp dirs and
everything (I'm thinking it could be to do with the temp_space and
workflow_run_dir variables, but you should check the others too).  The
important thing is that wherever you choose to put these directories,
make sure 1. they exist and 2. they have read/write permissions for
every user (i.e. chmod a+rw).  The ergatis pipelines are run by a
special apache user, rather than whatever your username is on the server.

Jason


On 6/13/11 3:43 PM, Muthuraman, Karthik Narayan (K) wrote:


> Hello
> I just installed ergatis and workflow manager.
>
> I'm not having much luck in building a simple pipeline with existing
> components. I followed the steps in
> ergatis/cgi/documentation.cgi?article=pipeline_creation, but I don't see
> the pipeline running.
>
> I just added the formatDB component on a fasta file. I included the
> $;FORMATDB_EXEC$; mentioned in /apps/ergatis/docs/formatdb.xml in
> /apps/ergatis/software.config and provided the full path to the fasta
> file in the interface.
>
> When I clicked on "Run Pipeline", the component seems to run forever.
> The fasta file is really small and the run should not take more than a
> few seconds.
>
> When I click on "view log" I get " : "pass file at
> /var/www/html/ergatis/cgi/view_formatted_log_source.cgi line 14.".
> It is expecting a file to be created under workflow/runtime which is not
> being created.
>
> Any suggestions ?
>
> Thanks for your time. I appreciate your help.
>
>
>
> Sincerely,
> Karthik Narayan
>
>
>
> ------------------------------------------------------------------------------
> EditLive Enterprise is the world's most technically advanced content
> authoring tool. Experience the power of Track Changes, Inline Image
> Editing and ensure content is compliant with Accessibility Checking.
> http://p.sf.net/sfu/ephox-dev2dev
> _______________________________________________
> Ergatis-users mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/ergatis-users


------------------------------------------------------------------------------
EditLive Enterprise is the world's most technically advanced content
authoring tool. Experience the power of Track Changes, Inline Image
Editing and ensure content is compliant with Accessibility Checking.
http://p.sf.net/sfu/ephox-dev2dev
_______________________________________________
Ergatis-users mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/ergatis-users

 


------------------------------------------------------------------------------
EditLive Enterprise is the world's most technically advanced content
authoring tool. Experience the power of Track Changes, Inline Image
Editing and ensure content is compliant with Accessibility Checking.
http://p.sf.net/sfu/ephox-dev2dev
_______________________________________________
Ergatis-users mailing list
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Re: running my first pipeline

Joshua Orvis
Hmm ... Could you post the output of the script somewhere?  It doesn't have a single overall PASS/FAIL as its output.  Instead, it lists the counts of successful or failed attempts that it checks for, including a warning count.

Joshua

On Tue, Jun 14, 2011 at 9:47 AM, Muthuraman, Karthik Narayan (K) <[hidden email]> wrote:

Thank you Joshua. I did try the ./check_installation script. It produced some warnings and error messages, but resulted in “PASS”.

 

Sincerely,
Karthik Narayan

 

From: Joshua Orvis [mailto:[hidden email]]
Sent: Tuesday, June 14, 2011 10:46 AM
To: [hidden email]; [hidden email]; Muthuraman, Karthik Narayan (K)
Subject: Re: [Ergatis-users] running my first pipeline

 

Karthik -

If the log file isn't even being created it looks like Workflow is failing to be invoked.  Did you try running the "check_installation.pl" script that's found in your install tarball?  You pass it your INI file and it attempts to check and make sure your directory permissions, etc. are set correctly.  That's the first starting point.

Joshua


On Mon, Jun 13, 2011 at 6:47 PM, Jason Kwan <[hidden email]> wrote:

Hi Karthik,

I have a vague recollection of running into a similar error message.  It
seems to be at a point in the cgi script where it is trying to write to
the scratch/tmp workflow space (although the devs should correct me if I
am wrong).  I would check through /<web documents
directory>/ergatis/cgi/ergatis.ini, and set all the tmp dirs and
everything (I'm thinking it could be to do with the temp_space and
workflow_run_dir variables, but you should check the others too).  The
important thing is that wherever you choose to put these directories,
make sure 1. they exist and 2. they have read/write permissions for
every user (i.e. chmod a+rw).  The ergatis pipelines are run by a
special apache user, rather than whatever your username is on the server.

Jason


On 6/13/11 3:43 PM, Muthuraman, Karthik Narayan (K) wrote:
> Hello
> I just installed ergatis and workflow manager.
>
> I'm not having much luck in building a simple pipeline with existing
> components. I followed the steps in
> ergatis/cgi/documentation.cgi?article=pipeline_creation, but I don't see
> the pipeline running.
>
> I just added the formatDB component on a fasta file. I included the
> $;FORMATDB_EXEC$; mentioned in /apps/ergatis/docs/formatdb.xml in
> /apps/ergatis/software.config and provided the full path to the fasta
> file in the interface.
>
> When I clicked on "Run Pipeline", the component seems to run forever.
> The fasta file is really small and the run should not take more than a
> few seconds.
>
> When I click on "view log" I get " : "pass file at
> /var/www/html/ergatis/cgi/view_formatted_log_source.cgi line 14.".
> It is expecting a file to be created under workflow/runtime which is not
> being created.


>
> Any suggestions ?
>
> Thanks for your time. I appreciate your help.
>
>
>
> Sincerely,
> Karthik Narayan
>
>
>
> ------------------------------------------------------------------------------
> EditLive Enterprise is the world's most technically advanced content
> authoring tool. Experience the power of Track Changes, Inline Image
> Editing and ensure content is compliant with Accessibility Checking.
> http://p.sf.net/sfu/ephox-dev2dev
> _______________________________________________
> Ergatis-users mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/ergatis-users


------------------------------------------------------------------------------
EditLive Enterprise is the world's most technically advanced content
authoring tool. Experience the power of Track Changes, Inline Image
Editing and ensure content is compliant with Accessibility Checking.
http://p.sf.net/sfu/ephox-dev2dev
_______________________________________________
Ergatis-users mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/ergatis-users

 



------------------------------------------------------------------------------
EditLive Enterprise is the world's most technically advanced content
authoring tool. Experience the power of Track Changes, Inline Image
Editing and ensure content is compliant with Accessibility Checking.
http://p.sf.net/sfu/ephox-dev2dev
_______________________________________________
Ergatis-users mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/ergatis-users