RE: Recursive implicit rules without explicit intermediates?

[Luke Goodsell]

Hi Pierre,

That's an interesting idea. However, the pipelines each need to be manually 
edited in a way that cannot be feasibly parameterised out. I'd have to write a 
different complex XSLT for each project, which could start getting burdensome.

I'll certainly consider it as a possible solution, though, as it would make 
report generation simpler.

Many thanks,
Luke


-----Original Message-----
From: address@hidden [mailto:address@hidden On Behalf Of Pierre Lindenbaum
Sent: 15 January 2015 17:30
To: address@hidden
Subject: Re: Recursive implicit rules without explicit intermediates?

Hi Luke,

I use Make to run my bioinformatics workflows.

As far as I understand your question, you're trying to generate a makefile for 
a complex structured model.

My makefile itself is generated with a XML file describing the experiment ...

    <?xml  version="1.0"  encoding="UTF-8"?>
    <model  name="myProject"  description="my project"  directory="OUT">
       <project  name="Proj1">
         <sample  name="Sample1">
           <fastq>
             <for>test/fastq/sample_1_01_R1.fastq.gz</for>
             <rev>test/fastq/sample_1_01_R2.fastq.gz</rev>
           </fastq>
           <fastq>
             <for>test/fastq/sample_1_02_R1.fastq.gz</for>
             <rev>test/fastq/sample_1_02_R2.fastq.gz</rev>
           </fastq>
         </sample>
         <sample  name="Sample2">
           <fastq>
             <for>test/fastq/sample_2_01_R1.fastq.gz</for>
             <rev>test/fastq/sample_2_01_R2.fastq.gz</rev>
           </fastq>
         </sample>
       </project>
    </model>




  and a XSLT stylesheet to transform XML to a Makefile.


       xsltproc --output makefile model2make.xsl model01.xml


An example for Next Generation Sequencing is posted at: 
https://github.com/lindenb/ngsxml

I also use apache velocity + json to generate my makefiles with 
https://github.com/lindenb/jsvelocity

Pierre L


> ------------------
>
> Message: 2
> Date: Thu, 15 Jan 2015 12:15:29 +0000
> From: Luke Goodsell<address@hidden> To:"address@hidden"  
> <address@hidden>
> Subject: Recursive implicit rules without explicit intermediates?
> Message-ID:
>       
> <address@hidden
> p.com>
>       
> Content-Type: text/plain; charset="us-ascii"
>
> Hi,
>
> Thanks in advance for taking the time to read and reply to my email.
>
> $ make --version
> GNU Make 4.0
> Built for x86_64-pc-linux-gnu
>
> Abstract:
>
> I'm writing a template makefile for performing similar - but different - 
> computational biology pipelines and am encountering an issue with recursive 
> implicit rules. Please can you suggest a solution that doesn't require 
> explicitly listing every intermediate target?
>
> Background:
>
> I'm writing a Makefile template that can be used for new projects. Each 
> project follows a very similar, path but with differences that must be 
> manually adapted. Each project has to perform similar tasks on each of number 
> of different 'sections', each of which has a number of different 'groups' 
> that each have a number of 'steps'. Each step cannot be run until the 
> previous step has run. The same is true of groups and sections.
>
>


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