Re: Recursive implicit rules without explicit intermediates?

[Pierre Lindenbaum]

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>
>         
> 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.