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RE: Recursive implicit rules without explicit intermediates?
From: |
Luke Goodsell |
Subject: |
RE: Recursive implicit rules without explicit intermediates? |
Date: |
Fri, 16 Jan 2015 10:44:25 +0000 |
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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