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: help-make-bounces+luke.goodsell=ogt....@gnu.org [mailto:help-make-bounces+luke.goodsell=ogt....@gnu.org] On Behalf Of Pierre Lindenbaum Sent: 15 January 2015 17:30 To: help-make@gnu.org 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<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.ogti > 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. > > _______________________________________________ Help-make mailing list Help-make@gnu.org https://lists.gnu.org/mailman/listinfo/help-make _______________________________________________ Help-make mailing list Help-make@gnu.org https://lists.gnu.org/mailman/listinfo/help-make
