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<luke.goods...@ogt.com>
To:"help-make@gnu.org" <help-make@gnu.org>
Subject: Recursive implicit rules without explicit intermediates?
Message-ID:
<7e96d1886e6b294ea4403ef577d92e8d511b9...@exchangeserver.internal.ogtip.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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