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From: | Pierre Lindenbaum |
Subject: | Re: Recursive implicit rules without explicit intermediates? |
Date: | Thu, 15 Jan 2015 18:29:30 +0100 |
User-agent: | Mozilla/5.0 (X11; Linux i686; rv:31.0) Gecko/20100101 Thunderbird/31.3.0 |
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.xmlAn 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.
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