From morecmenpasts at wildmail.com  Sun Feb  1 06:06:39 2004
From: morecmenpasts at wildmail.com (E.bachman)
Date: Sat Jan 31 21:12:05 2004
Subject: [Bioperl-pipeline] Cum And Look Like A P0RN STAR!!!!!!!!
	sluggishflaxen
Message-ID: <vpcalbmqu.6876529erxikiaaha@E.bachmanywlwp>

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From moreincheselect at wildmail.com  Sun Feb  1 23:17:00 2004
From: moreincheselect at wildmail.com (Bionor)
Date: Sun Feb  1 23:28:43 2004
Subject: [Bioperl-pipeline] 
	NaturalGain+ , What more do you want?      buster
Message-ID: <tfcdfyclwd.848673njkazccduo@Bionorepzgbw>

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From 01agebackHedda at rocketmail.com  Mon Feb  2 16:04:34 2004
From: 01agebackHedda at rocketmail.com (Dzhao)
Date: Tue Feb  3 00:09:37 2004
Subject: [Bioperl-pipeline] Wanna look younger again??    Fargo
Message-ID: <apptwtqyav.60595gqfedxof@Dzhaohupaidftg>

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From BigJ0hnsonfoiling at wildmail.com  Wed Feb  4 06:39:34 2004
From: BigJ0hnsonfoiling at wildmail.com (Vince)
Date: Wed Feb  4 06:45:46 2004
Subject: [Bioperl-pipeline] Enlarge Ur C0ck By 3+inches  kernels
Message-ID: <ipllgzhuys.68987ubrpwsnru@Vincemdbrhmxymy>

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From dehneg at labri.fr  Tue Feb 10 12:31:42 2004
From: dehneg at labri.fr (Alexandre Dehne)
Date: Tue Feb 10 12:37:46 2004
Subject: [Bioperl-pipeline] creating jobs, job_setup
Message-ID: <1076434302.1593.276.camel@houat.labri.fr>

Hi,

First, I would like to congratulate the Biopipe team for having created such a useful tool.


The context : 
For several reasons (some goods and some not so good), some of my runnables take nothing in input and return nothing. 

The problem : 
This type of runnables does not match the biopipe "spirit", so it is a problem to create jobs for these runnables via the "create_job" function which needs a array input.

The "temporary" unrighteous solution : 
I have created an InputCreate module named setup_nothing which creates a void input like the following :
    my @input=$self->create_input("nothing",'',"infile");
    my $job   = $self->create_job($next_anal,\@input);
    $self->dbadaptor->get_JobAdaptor->store($job);
This way, I launch one job on my analysis as well as on the following ones by placing "<action>COPY_ID_FILE</action>" in their respective rules in the XML file.


The questions : 
Is there a clean way to create jobs without any input (a just_do_it function ?) ? 
Perhaps the <job_setup> mark in the XML file ?
Also, could someone tell me more about this <job_setup> mark ??? 


Thank you in advance


Alexandre




From kumark at cshl.org  Tue Feb 10 18:30:46 2004
From: kumark at cshl.org (Kiran Kumar)
Date: Tue Feb 10 18:36:46 2004
Subject: [Bioperl-pipeline] creating jobs, job_setup
In-Reply-To: <1076434302.1593.276.camel@houat.labri.fr>
Message-ID: <Pine.GSO.4.05.10402101754130.21872-100000@phage.cshl.edu>


Hi Alexandre,
It's nice to know that it fits into your work.

In short, you would be able to create job without inputs. The direct way
would be 'not to pass' any inputs to "create_job" function.

      my $job   = $self->create_job($next_anal);
      $self->dbadaptor->get_JobAdaptor->store($job);
That should make it 'righteous' :-)..

Since you are following the Biopipe spirit, let me go on to explain the
other aspects too.


On the xml level, you are right that the <job_setup> tag could be used for
this purpose.
The <job_setup> provides for specifying jobs directly inside the XML file
without using a Datamonger/InputCreate. Ofcourse, this is convinient if
the number of jobs are handful which otherwise would make the XML file
very lengthy. This feature is still there but has not been tested for long
time. We have stopped using this feature for a drawback it poses towards
the biopipe spirit which is as follows.

If the job needs inputs, and it is specified using job_setup options,
the xml file becomes too specific and anyone else trying to re-use it
would have to change all the input_ids each time they need to run for
different sets of inputs. The datamonger/InputCreate on the other hand,
provides for the clean separation of input names from the xml pipeline
specification. The InputCreates are expected to read the input_names for
the the jobs they are gonna create from a file or directory or somewhere
(this location for the input_names is specified as the input_create's
parameters in the xml file).

Hope I havent left you more confused than before!

Cheers,
Kiran


>Hi,
>
>First, I would like to congratulate the Biopipe team for having created such a useful tool.
>
>
>The context : 
>For several reasons (some goods and some not so good), some of my runnables take nothing in input and return nothing. 
>
>The problem : 
>This type of runnables does not match the biopipe "spirit", so it is a problem to create jobs for these runnables via the "create_job" function which needs a array input.
>
>The "temporary" unrighteous solution : 
>I have created an InputCreate module named setup_nothing which creates a void input like the following :
>    my @input=$self->create_input("nothing",'',"infile");
>    my $job   = $self->create_job($next_anal,\@input);
>    $self->dbadaptor->get_JobAdaptor->store($job);
>This way, I launch one job on my analysis as well as on the following ones by placing "<action>COPY_ID_FILE</action>" in their respective rules in the XML file.
>
>
>The questions : 
>Is there a clean way to create jobs without any input (a just_do_it function ?) ? 
>Perhaps the <job_setup> mark in the XML file ?
>Also, could someone tell me more about this <job_setup> mark ??? 
>
>
>Thank you in advance
>
>
>Alexandre
>
>
>
>
>_______________________________________________
>bioperl-pipeline mailing list
>bioperl-pipeline@bioperl.org
>http://bioperl.org/mailman/listinfo/bioperl-pipeline
>

From dehneg at labri.fr  Thu Feb 12 08:48:52 2004
From: dehneg at labri.fr (Alexandre Dehne)
Date: Thu Feb 12 08:55:00 2004
Subject: [Bioperl-pipeline] creating jobs, job_setup
In-Reply-To: <Pine.GSO.4.05.10402101754130.21872-100000@phage.cshl.edu>
References: <Pine.GSO.4.05.10402101754130.21872-100000@phage.cshl.edu>
Message-ID: <1076593731.1593.358.camel@houat.labri.fr>

Hi Kiran,

Thank you for answering me.
Actually, your solution is very clean but, by using it, other problems
came up.

Here is the current situation:
So, I start a job on my first analysis with your suggestion. Then, more 
jobs on other analysis are created by placing
"<action>COPY_ID_FILE</action>" or "<action>COPY_ID</action>" in their
respective rules in the XML file. 
(Remember that for now, all of my analysis do not take any input and do
not give any output. So, this way, everything is fine and work well.)

Here comes the problem when I want to use an analysis that needs an
input. For that, I am using the data monger. Since the data monger needs
an input, it therefore does not work. So, I am trying to create this
input by using the following <input> mark:

...
   <analysis id="4">
      <data_monger>
        <input>
          <name>$input_description</name>
          <iohandler>1</iohandler>
        </input>
        <input_create>
....


My initial data monger (analysis N.1) and the one previously described
(analysis N.4) are now called at the beginning of the pipeline.
But, the analysis N.4 has to be called after the third one as I
specified it in the rules.

Do you have any suggestion on how to solve my problem and why the rules
are not followed ?
Please let me know if I am not clear.

Thank you in advance,

Alexandre



On Wed, 2004-02-11 at 00:30, Kiran Kumar wrote:
> Hi Alexandre,
> It's nice to know that it fits into your work.
> 
> In short, you would be able to create job without inputs. The direct way
> would be 'not to pass' any inputs to "create_job" function.
> 
>       my $job   = $self->create_job($next_anal);
>       $self->dbadaptor->get_JobAdaptor->store($job);
> That should make it 'righteous' :-)..
> 
> Since you are following the Biopipe spirit, let me go on to explain the
> other aspects too.
> 
> 
> On the xml level, you are right that the <job_setup> tag could be used for
> this purpose.
> The <job_setup> provides for specifying jobs directly inside the XML file
> without using a Datamonger/InputCreate. Ofcourse, this is convinient if
> the number of jobs are handful which otherwise would make the XML file
> very lengthy. This feature is still there but has not been tested for long
> time. We have stopped using this feature for a drawback it poses towards
> the biopipe spirit which is as follows.
> 
> If the job needs inputs, and it is specified using job_setup options,
> the xml file becomes too specific and anyone else trying to re-use it
> would have to change all the input_ids each time they need to run for
> different sets of inputs. The datamonger/InputCreate on the other hand,
> provides for the clean separation of input names from the xml pipeline
> specification. The InputCreates are expected to read the input_names for
> the the jobs they are gonna create from a file or directory or somewhere
> (this location for the input_names is specified as the input_create's
> parameters in the xml file).
> 
> Hope I havent left you more confused than before!
> 
> Cheers,
> Kiran
> 
> 
> >Hi,
> >
> >First, I would like to congratulate the Biopipe team for having created such a useful tool.
> >
> >
> >The context : 
> >For several reasons (some goods and some not so good), some of my runnables take nothing in input and return nothing. 
> >
> >The problem : 
> >This type of runnables does not match the biopipe "spirit", so it is a problem to create jobs for these runnables via the "create_job" function which needs a array input.
> >
> >The "temporary" unrighteous solution : 
> >I have created an InputCreate module named setup_nothing which creates a void input like the following :
> >    my @input=$self->create_input("nothing",'',"infile");
> >    my $job   = $self->create_job($next_anal,\@input);
> >    $self->dbadaptor->get_JobAdaptor->store($job);
> >This way, I launch one job on my analysis as well as on the following ones by placing "<action>COPY_ID_FILE</action>" in their respective rules in the XML file.
> >
> >
> >The questions : 
> >Is there a clean way to create jobs without any input (a just_do_it function ?) ? 
> >Perhaps the <job_setup> mark in the XML file ?
> >Also, could someone tell me more about this <job_setup> mark ??? 
> >
> >
> >Thank you in advance
> >
> >
> >Alexandre
> >
> >
> >
> >
> >_______________________________________________
> >bioperl-pipeline mailing list
> >bioperl-pipeline@bioperl.org
> >http://bioperl.org/mailman/listinfo/bioperl-pipeline
> >
> 

From shawnh at fugu-sg.org  Fri Feb 13 03:18:58 2004
From: shawnh at fugu-sg.org (Shawn Hoon)
Date: Fri Feb 13 03:24:54 2004
Subject: [Bioperl-pipeline] creating jobs, job_setup
In-Reply-To: <1076593731.1593.358.camel@houat.labri.fr>
References: <Pine.GSO.4.05.10402101754130.21872-100000@phage.cshl.edu>
	<1076593731.1593.358.camel@houat.labri.fr>
Message-ID: <45CB6AED-5DFD-11D8-A4FD-000A95783436@fugu-sg.org>

Hi Alexandre,
	okay this is what I gather you are trying to do:

Run analysis 1 -> 2 -> 3 -> 4

The question is what are your inputs? are u running the four analysis 
on the same input type? for example, you
have four blast analysis that you do on  sequences? If so, then what 
you would do is use a input create/data monger to
create inputs for analysis 1. Then in your rules you would specify 
COPY_ID for analysis 1 -> 2 and 2->3 and 3->4
then the input id will be transferred between analysis.

If your input  for analysis 2 for example is different from that of 
analysis 1, then you need to do something different.
For this, there are 2 options:

	1) If you require that the analysis 1 is completed before 2 is 
completed, then you need an analysis in between 1 and 2 ( so as a 
result 2 becomes 3)
	     Analysis 2 would now be an input_create which knows how to create 
inputs for analysis 2. (Basically we are assuming the this input 
creation is linked to
   	     the input 1 of analysis 1.
	2) If you require that all of the inputs from analysis 1 is completed 
before any analysis 2 jobs are started, you can do a rule WAITFORALL 
which would then launch
     	     a job of analysis 2 (which may or may not be a input create).

for your definition below, I don't see why analysis 4 should be 
executed at startup. Can you provide the xml file?
shawn


On Feb 12, 2004, at 5:48 AM, Alexandre Dehne wrote:

> Hi Kiran,
>
> Thank you for answering me.
> Actually, your solution is very clean but, by using it, other problems
> came up.
>
> Here is the current situation:
> So, I start a job on my first analysis with your suggestion. Then, more
> jobs on other analysis are created by placing
> "<action>COPY_ID_FILE</action>" or "<action>COPY_ID</action>" in their
> respective rules in the XML file.
> (Remember that for now, all of my analysis do not take any input and do
> not give any output. So, this way, everything is fine and work well.)
>
> Here comes the problem when I want to use an analysis that needs an
> input. For that, I am using the data monger. Since the data monger 
> needs
> an input, it therefore does not work. So, I am trying to create this
> input by using the following <input> mark:
>
> ...
>    <analysis id="4">
>       <data_monger>
>         <input>
>           <name>$input_description</name>
>           <iohandler>1</iohandler>
>         </input>
>         <input_create>
> ....
>
>
> My initial data monger (analysis N.1) and the one previously described
> (analysis N.4) are now called at the beginning of the pipeline.
> But, the analysis N.4 has to be called after the third one as I
> specified it in the rules.
>
> Do you have any suggestion on how to solve my problem and why the rules
> are not followed ?
> Please let me know if I am not clear.
>
> Thank you in advance,
>
> Alexandre
>
>
>
> On Wed, 2004-02-11 at 00:30, Kiran Kumar wrote:
>> Hi Alexandre,
>> It's nice to know that it fits into your work.
>>
>> In short, you would be able to create job without inputs. The direct 
>> way
>> would be 'not to pass' any inputs to "create_job" function.
>>
>>       my $job   = $self->create_job($next_anal);
>>       $self->dbadaptor->get_JobAdaptor->store($job);
>> That should make it 'righteous' :-)..
>>
>> Since you are following the Biopipe spirit, let me go on to explain 
>> the
>> other aspects too.
>>
>>
>> On the xml level, you are right that the <job_setup> tag could be 
>> used for
>> this purpose.
>> The <job_setup> provides for specifying jobs directly inside the XML 
>> file
>> without using a Datamonger/InputCreate. Ofcourse, this is convinient 
>> if
>> the number of jobs are handful which otherwise would make the XML file
>> very lengthy. This feature is still there but has not been tested for 
>> long
>> time. We have stopped using this feature for a drawback it poses 
>> towards
>> the biopipe spirit which is as follows.
>>
>> If the job needs inputs, and it is specified using job_setup options,
>> the xml file becomes too specific and anyone else trying to re-use it
>> would have to change all the input_ids each time they need to run for
>> different sets of inputs. The datamonger/InputCreate on the other 
>> hand,
>> provides for the clean separation of input names from the xml pipeline
>> specification. The InputCreates are expected to read the input_names 
>> for
>> the the jobs they are gonna create from a file or directory or 
>> somewhere
>> (this location for the input_names is specified as the input_create's
>> parameters in the xml file).
>>
>> Hope I havent left you more confused than before!
>>
>> Cheers,
>> Kiran
>>
>>
>>> Hi,
>>>
>>> First, I would like to congratulate the Biopipe team for having 
>>> created such a useful tool.
>>>
>>>
>>> The context :
>>> For several reasons (some goods and some not so good), some of my 
>>> runnables take nothing in input and return nothing.
>>>
>>> The problem :
>>> This type of runnables does not match the biopipe "spirit", so it is 
>>> a problem to create jobs for these runnables via the "create_job" 
>>> function which needs a array input.
>>>
>>> The "temporary" unrighteous solution :
>>> I have created an InputCreate module named setup_nothing which 
>>> creates a void input like the following :
>>>    my @input=$self->create_input("nothing",'',"infile");
>>>    my $job   = $self->create_job($next_anal,\@input);
>>>    $self->dbadaptor->get_JobAdaptor->store($job);
>>> This way, I launch one job on my analysis as well as on the 
>>> following ones by placing "<action>COPY_ID_FILE</action>" in their 
>>> respective rules in the XML file.
>>>
>>>
>>> The questions :
>>> Is there a clean way to create jobs without any input (a just_do_it 
>>> function ?) ?
>>> Perhaps the <job_setup> mark in the XML file ?
>>> Also, could someone tell me more about this <job_setup> mark ???
>>>
>>>
>>> Thank you in advance
>>>
>>>
>>> Alexandre
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> bioperl-pipeline mailing list
>>> bioperl-pipeline@bioperl.org
>>> http://bioperl.org/mailman/listinfo/bioperl-pipeline
>>>
>>
>
> _______________________________________________
> bioperl-pipeline mailing list
> bioperl-pipeline@bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-pipeline
>

From kokcowardly at byke.com  Tue Feb 17 14:44:13 2004
From: kokcowardly at byke.com (Chandiwana)
Date: Tue Feb 17 13:45:05 2004
Subject: [Bioperl-pipeline] freewheel CheapPharmacy killer
Message-ID: <kfuynqvi.005009ozxfd@Chandiwanazcodn>

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From m_conte at hotmail.com  Wed Feb 18 12:23:17 2004
From: m_conte at hotmail.com (matthieu CONTE)
Date: Wed Feb 18 12:29:34 2004
Subject: [Bioperl-pipeline] develop new module
Message-ID: <BAY12-F55Ua8d9Ee4za00036c7c@hotmail.com>

Hi,
I'm trying to develop a module for a java program.
Is there others wrappers in bioperl-run that work on java apps that Eponine 
and Vista?


-----------------------------------------------------------
Matthieu CONTE
M. Sc. in Bioinformatics from SIB

CIRAD-Biotrop TA40/03
Avenue Agropolis
34398 Montpellier Cedex 5
FRANCE

m_conte@hotmail.com
tel: (33)04 67 61 60 21
fax :(33) 4 67 61 56 05

-----------------------------------------------------------

_________________________________________________________________
MSN Search, le moteur de recherche qui pense comme vous ! 
http://search.msn.fr/worldwide.asp

From shawnh at stanford.edu  Wed Feb 18 13:13:18 2004
From: shawnh at stanford.edu (Shawn Hoon)
Date: Wed Feb 18 13:19:29 2004
Subject: [Bioperl-pipeline] develop new module
In-Reply-To: <BAY12-F55Ua8d9Ee4za00036c7c@hotmail.com>
References: <BAY12-F55Ua8d9Ee4za00036c7c@hotmail.com>
Message-ID: <20DEEEC4-623E-11D8-A4FD-000A95783436@stanford.edu>

I think these two are the only ones.

cheers,

shawn

On Feb 18, 2004, at 9:23 AM, matthieu CONTE wrote:

> Hi,
> I'm trying to develop a module for a java program.
> Is there others wrappers in bioperl-run that work on java apps that 
> Eponine and Vista?
>
>
> -----------------------------------------------------------
> Matthieu CONTE
> M. Sc. in Bioinformatics from SIB
>
> CIRAD-Biotrop TA40/03
> Avenue Agropolis
> 34398 Montpellier Cedex 5
> FRANCE
>
> m_conte@hotmail.com
> tel: (33)04 67 61 60 21
> fax :(33) 4 67 61 56 05
>
> -----------------------------------------------------------
>
> _________________________________________________________________
> MSN Search, le moteur de recherche qui pense comme vous ! 
> http://search.msn.fr/worldwide.asp
>
> _______________________________________________
> bioperl-pipeline mailing list
> bioperl-pipeline@bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-pipeline

From juguang at tll.org.sg  Wed Feb 18 21:11:55 2004
From: juguang at tll.org.sg (Juguang Xiao)
Date: Wed Feb 18 21:18:08 2004
Subject: [Bioperl-pipeline] develop new module
In-Reply-To: <BAY12-F55Ua8d9Ee4za00036c7c@hotmail.com>
Message-ID: <FD315F44-6280-11D8-A4BC-000A957702FE@tll.org.sg>

Let us know your java program and we would like to compose the wrapper 
for you.

Juguang

On Thursday, February 19, 2004, at 01:23  am, matthieu CONTE wrote:

> Hi,
> I'm trying to develop a module for a java program.
> Is there others wrappers in bioperl-run that work on java apps that 
> Eponine and Vista?
>
>
> -----------------------------------------------------------
> Matthieu CONTE
> M. Sc. in Bioinformatics from SIB
>
> CIRAD-Biotrop TA40/03
> Avenue Agropolis
> 34398 Montpellier Cedex 5
> FRANCE
>
> m_conte@hotmail.com
> tel: (33)04 67 61 60 21
> fax :(33) 4 67 61 56 05
>
> -----------------------------------------------------------
>
> _________________________________________________________________
> MSN Search, le moteur de recherche qui pense comme vous ! 
> http://search.msn.fr/worldwide.asp
>
> _______________________________________________
> bioperl-pipeline mailing list
> bioperl-pipeline@bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-pipeline
>
>
Juguang Xiao

From MRBATESALAN at netscape.net  Mon Feb 23 08:33:32 2004
From: MRBATESALAN at netscape.net (MRBATESALAN@netscape.net)
Date: Mon Feb 23 08:39:38 2004
Subject: [Bioperl-pipeline] REPLY SOON
Message-ID: <APMS9x6HHGNZ4mF1IT100001502@apms.apms.si>

Dear Friend,

As you read this, I don't want you to feel sorry for 
me, because, I believe everyone will die someday. 
My name is BATES ALAN a merchant in Dubai, in the 
U.A.E.I have been diagnosed with Esophageal cancer.
It has defiled all forms of medical treatment, and right now 
I have only about a few months to live, according to medical experts. 
I have not particularly lived my life so well, as I 
never really cared for anyone(not even myself)but my 
business. Though I am very rich, I was never 
generous, I was always hostile to people and only 
focused on my business as that was the only thing I 
cared for. But now I regret all this as I now know 
that there is more to life than just wanting to have 
or make all the money in the world. 
I believe when God gives me a second chance to come 
to this world I would live my life a different way 
from how I have lived it. Now that God has called 
me, I have willed and given most of my property 
and assets to my immediate and extended family 
members as well as a few close friends. 
I want God to be merciful to me and accept my soul 
so, I have decided to give alms to charity 
organizations, as I want this to be one of the last 
good deeds I do on earth. So far, I have distributed 
money to some charity organizations in the U.A.E, 
Algeria and Malaysia. Now that my health has 
deteriorated so badly, I cannot do this myself 
anymore. I once asked members of my family to close one 
of my accounts and distribute the money which I have 
there to charity organization in Bulgaria and 
Pakistan, they refused and kept the money to 
themselves. Hence, I do not trust them anymore, as 
they seem not to be contended with what I have left 
for them. 
The last of my money which no one knows of is the 
huge cash deposit of eighteen million dollars 
$18,000,000,00 that I have with a finance/Security Company 
abroad. I will want you to help me collect this deposit 
and dispatched it to charity organizations.
I have set aside 10% for you and for your time.
God be with you. 
BATES ALAN

From dehneg at labri.fr  Wed Feb 18 09:36:14 2004
From: dehneg at labri.fr (Alexandre Dehne)
Date: Fri Feb 27 10:07:01 2004
Subject: [Bioperl-pipeline] creating jobs, job_setup
In-Reply-To: <45CB6AED-5DFD-11D8-A4FD-000A95783436@fugu-sg.org>
References: <Pine.GSO.4.05.10402101754130.21872-100000@phage.cshl.edu>
	<1076593731.1593.358.camel@houat.labri.fr>
	<45CB6AED-5DFD-11D8-A4FD-000A95783436@fugu-sg.org>
Message-ID: <1077114973.3020.339.camel@houat.labri.fr>

Hi,

Please excuse me for not being clear enough in my last mail. So I am
going to *try* to be more explicite. I am introducing now on three new
pipelines (A, B and C) derived from the one I mentionned in my last
email to explain my problems (you can forget the pipeline in my last
email, I am introducing  the new ones entirely ; the xml files are
attached).
The pipelines A and B allow me to show you the problem that came up
using Kiran's solution. The pipelines A and C help me to explain the way
the rules were not followed.

Let's start with the descriptions of the pipelines A, B and C.
First, the common structure of A, B and C :
run analysis : 1->2->3->4->5
analysis 1 : datamonger
analysis 2 and 3 : analysis that take nothing on input and ouput nothing
(using CAAT-Box program in my case).
analysis 4 : datamonger
analysis 5 : analysis that need an input (from analysis 4), using blast
for example.


Then the differences between the analysis from A, B and C :

# analysis 1 from A and C (my old solution) : a datamonger that uses an
InputCreate module named setup_nothing which creates a "void" input like
the following :
  my @input=$self->create_input("nothing",'',"infile");
  my $job   = $self->create_job($next_anal,\@input);
  $self->dbadaptor->get_JobAdaptor->store($job);

# analysis 1 from B (Kiran's solution) : a datamonger that uses an
InputCreate module named setup_nothing_kiran which creates a void input
like the following :
   my $job   = $self->create_job($next_anal);
   $self->dbadaptor->get_JobAdaptor->store($job);

# analysis 2 and 3 (from A, B and C) : nothing special exept that the
<action> tag has to be  "COPY_ID_FILE" in A and B, but can be
indeferently "COPY_ID_FILE"  or "COPY_ID" in C.

# analysis 4 from A and B : a datamonger using an InputCreate module
which creates jobs with an input (for example the module setup_initial).
Please note that, contrary to the analysis 4 from A, the <input> tag is
outside the <data_monger> tag:
...
   <analysis id="4">
      <input>
         <name>$input_description</name>
         <iohandler>1</iohandler>
      </input>
      <data_monger>
        <input_create>
          <module>setup_initial</module>
          <rank>1</rank>
 ....

# analysis 4 from C : a datamonger using an InputCreate module which
creates jobs with an input (for example the module setup_initial).
Please note that, contrary to the analysis 4 from A and B, the <input>
tag is inside the <data_monger> tag :
...
   <analysis id="4">
      <data_monger>
        <input>
          <name>$input_description</name>
          <iohandler>1</iohandler>
        </input>
        <input_create>
          <module>setup_initial</module>
          <rank>1</rank>
 ....




# analysis 5 (from A, B and C): nothing special, the same blast analysis
as in the example blast_db_file.xml.





Okay, now you know all about the pipelines A, B and C.
The pipeline A  is the one I precedently used to create void inputs (via
the module setup_nothing) and the pipeline B is the Kiran's way (via the
module setup_nothing). I really like Kiran's solution but without any
input the analysis 4 returns the following error to me:
======== "
  READING: Lost the will to live Error. Problems with runnableDB
fetching input
   [
   ------------- EXCEPTION: Bio::Root::Exception -------------
   MSG: Runnable Bio::Pipeline::Runnable::DataMonger=HASH(0x89f1b98)
cannot call
   STACK: Error::throw
   STACK: Bio::Root::Root::throw
/usr/lib/perl5/site_perl/5.8.0/Bio/Root/Root.pm:342
   STACK: Bio::Pipeline::RunnableDB::setup_runnable_inputs
/var/opt/Genolevures/src/biopipe-bundle-0.1/bioperl-pipeline/Bio/Pipeline/RunnableDB.pm:244
   STACK: Bio::Pipeline::RunnableDB::fetch_input
/var/opt/Genolevures/src/biopipe-bundle-0.1/bioperl-pipeline/Bio/Pipeline/RunnableDB.pm:485
   ......
" ============

My questions concerning Kiran's solution are :
- How can I manage this problem (using the data monger after an analysis
which outputs nothing ) ?
- Is there another <action> tag (different from "COPY_ID" or
"COPY_ID_FILE") which does not use the concept of copying an input
(which does not exist in my case) ?




That was the questions using pipeline A and B. Now, I focus on pipelines
A and C to show how the rules are not followed. Indeed, by running
pipeline C, the analysis 4 starts just after the analysis 1 which
contradicts the rules. Do you have an explanation ? Anyway, I
overturned this problem by using the pipeline A which consists in
writing the <input> tag outside the <data_monger> tag for the analysis 4.



I hope I am clear enough.
Thanks in advance.


Alexandre






On Fri, 2004-02-13 at 09:18, Shawn Hoon wrote:
> Hi Alexandre,
> 	okay this is what I gather you are trying to do:
> 
> Run analysis 1 -> 2 -> 3 -> 4
> 
> The question is what are your inputs? are u running the four analysis 
> on the same input type? for example, you
> have four blast analysis that you do on  sequences? If so, then what 
> you would do is use a input create/data monger to
> create inputs for analysis 1. Then in your rules you would specify 
> COPY_ID for analysis 1 -> 2 and 2->3 and 3->4
> then the input id will be transferred between analysis.
> 
> If your input  for analysis 2 for example is different from that of 
> analysis 1, then you need to do something different.
> For this, there are 2 options:
> 
> 	1) If you require that the analysis 1 is completed before 2 is 
> completed, then you need an analysis in between 1 and 2 ( so as a 
> result 2 becomes 3)
> 	     Analysis 2 would now be an input_create which knows how to create 
> inputs for analysis 2. (Basically we are assuming the this input 
> creation is linked to
>    	     the input 1 of analysis 1.
> 	2) If you require that all of the inputs from analysis 1 is completed 
> before any analysis 2 jobs are started, you can do a rule WAITFORALL 
> which would then launch
>      	     a job of analysis 2 (which may or may not be a input create).
> 
> for your definition below, I don't see why analysis 4 should be 
> executed at startup. Can you provide the xml file?
> shawn
> 
> 
> On Feb 12, 2004, at 5:48 AM, Alexandre Dehne wrote:
> 
> > Hi Kiran,
> >
> > Thank you for answering me.
> > Actually, your solution is very clean but, by using it, other problems
> > came up.
> >
> > Here is the current situation:
> > So, I start a job on my first analysis with your suggestion. Then, more
> > jobs on other analysis are created by placing
> > "<action>COPY_ID_FILE</action>" or "<action>COPY_ID</action>" in their
> > respective rules in the XML file.
> > (Remember that for now, all of my analysis do not take any input and do
> > not give any output. So, this way, everything is fine and work well.)
> >
> > Here comes the problem when I want to use an analysis that needs an
> > input. For that, I am using the data monger. Since the data monger 
> > needs
> > an input, it therefore does not work. So, I am trying to create this
> > input by using the following <input> mark:
> >
> > ...
> >    <analysis id="4">
> >       <data_monger>
> >         <input>
> >           <name>$input_description</name>
> >           <iohandler>1</iohandler>
> >         </input>
> >         <input_create>
> > ....
> >
> >
> > My initial data monger (analysis N.1) and the one previously described
> > (analysis N.4) are now called at the beginning of the pipeline.
> > But, the analysis N.4 has to be called after the third one as I
> > specified it in the rules.
> >
> > Do you have any suggestion on how to solve my problem and why the rules
> > are not followed ?
> > Please let me know if I am not clear.
> >
> > Thank you in advance,
> >
> > Alexandre
> >
> >
> >
> > On Wed, 2004-02-11 at 00:30, Kiran Kumar wrote:
> >> Hi Alexandre,
> >> It's nice to know that it fits into your work.
> >>
> >> In short, you would be able to create job without inputs. The direct 
> >> way
> >> would be 'not to pass' any inputs to "create_job" function.
> >>
> >>       my $job   = $self->create_job($next_anal);
> >>       $self->dbadaptor->get_JobAdaptor->store($job);
> >> That should make it 'righteous' :-)..
> >>
> >> Since you are following the Biopipe spirit, let me go on to explain 
> >> the
> >> other aspects too.
> >>
> >>
> >> On the xml level, you are right that the <job_setup> tag could be 
> >> used for
> >> this purpose.
> >> The <job_setup> provides for specifying jobs directly inside the XML 
> >> file
> >> without using a Datamonger/InputCreate. Ofcourse, this is convinient 
> >> if
> >> the number of jobs are handful which otherwise would make the XML file
> >> very lengthy. This feature is still there but has not been tested for 
> >> long
> >> time. We have stopped using this feature for a drawback it poses 
> >> towards
> >> the biopipe spirit which is as follows.
> >>
> >> If the job needs inputs, and it is specified using job_setup options,
> >> the xml file becomes too specific and anyone else trying to re-use it
> >> would have to change all the input_ids each time they need to run for
> >> different sets of inputs. The datamonger/InputCreate on the other 
> >> hand,
> >> provides for the clean separation of input names from the xml pipeline
> >> specification. The InputCreates are expected to read the input_names 
> >> for
> >> the the jobs they are gonna create from a file or directory or 
> >> somewhere
> >> (this location for the input_names is specified as the input_create's
> >> parameters in the xml file).
> >>
> >> Hope I havent left you more confused than before!
> >>
> >> Cheers,
> >> Kiran
> >>
> >>
> >>> Hi,
> >>>
> >>> First, I would like to congratulate the Biopipe team for having 
> >>> created such a useful tool.
> >>>
> >>>
> >>> The context :
> >>> For several reasons (some goods and some not so good), some of my 
> >>> runnables take nothing in input and return nothing.
> >>>
> >>> The problem :
> >>> This type of runnables does not match the biopipe "spirit", so it is 
> >>> a problem to create jobs for these runnables via the "create_job" 
> >>> function which needs a array input.
> >>>
> >>> The "temporary" unrighteous solution :
> >>> I have created an InputCreate module named setup_nothing which 
> >>> creates a void input like the following :
> >>>    my @input=$self->create_input("nothing",'',"infile");
> >>>    my $job   = $self->create_job($next_anal,\@input);
> >>>    $self->dbadaptor->get_JobAdaptor->store($job);
> >>> This way, I launch one job on my analysis as well as on the 
> >>> following ones by placing "<action>COPY_ID_FILE</action>" in their 
> >>> respective rules in the XML file.
> >>>
> >>>
> >>> The questions :
> >>> Is there a clean way to create jobs without any input (a just_do_it 
> >>> function ?) ?
> >>> Perhaps the <job_setup> mark in the XML file ?
> >>> Also, could someone tell me more about this <job_setup> mark ???
> >>>
> >>>
> >>> Thank you in advance
> >>>
> >>>
> >>> Alexandre
> >>>
> >>>
> >>>
> >>>
> >>> _______________________________________________
> >>> bioperl-pipeline mailing list
> >>> bioperl-pipeline@bioperl.org
> >>> http://bioperl.org/mailman/listinfo/bioperl-pipeline
> >>>
> >>
> >
> > _______________________________________________
> > bioperl-pipeline mailing list
> > bioperl-pipeline@bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-pipeline
> >
> 
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From faga at cshl.org  Fri Feb 27 10:16:59 2004
From: faga at cshl.org (Ben Faga)
Date: Fri Feb 27 10:24:23 2004
Subject: [Bioperl-pipeline] typo in XML_README.html
Message-ID: <1077895019.6069.18.camel@ricotta>

Hi,

I hope this doesn't go to a mailing list because I'm just reporting a
typo.

In the description of <global> at
http://www.biopipe.org/docs/html/XML_README.html, the sentence "This
makes path definitions and centralized and users of the XML template
should only need to modify things here" has an extra "and" in it, I
think.

Ben