Ben Woodcroft <b.woodcr...@uq.edu.au> writes: > Updated patch attached.
Much better, thanks! > In answer to my own question >> During development of this patch I noticed badly specified system* > does not throw an error - is there a way to do this so? > > One way is to replace system* with (zero? (system* with that being the > return value of the lambda - there's an example in the attached patch. Yes, that's a good option. Please see below for more comments. > From d18f50e17547fa741569be109b31ef13c79b3d97 Mon Sep 17 00:00:00 2001 > From: Ben Woodcroft <donttrust...@gmail.com> > Date: Sun, 21 Jun 2015 09:02:26 +1000 > Subject: [PATCH] gnu: Add fasttree Nitpick: we prefer to add a period "." to the end of the summary line above. > > * gnu/packages/bioinformatics.scm (fasttree): New variable. > --- > gnu/packages/bioinformatics.scm | 60 > +++++++++++++++++++++++++++++++++++++++++ > 1 file changed, 60 insertions(+) > > diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm > index 12c9175..0aacce7 100644 > --- a/gnu/packages/bioinformatics.scm > +++ b/gnu/packages/bioinformatics.scm > @@ -780,6 +780,66 @@ analysis (from RNA-Seq), transcription factor binding > quantification in > ChIP-Seq, and analysis of metagenomic data.") > (license license:artistic2.0))) > > +(define-public fasttree > + (package > + (name "fasttree") > + (version "2.1.8") > + (source (origin > + (method url-fetch) > + (uri (string-append > + "http://www.microbesonline.org/fasttree/FastTree-"; > + version ".c" > + )) In the Scheme world, it is considered bad form to leave close parentheses on their own line. Please move these to the previous line, like this: version ".c")) > + (replace 'build > + (lambda* (#:key source #:allow-other-keys) > + (and (zero? (system* "gcc" > + "-O3" > + "-finline-functions" > + "-funroll-loops" > + "-Wall" > + "-o" > + "FastTree" > + source > + "-lm")) > + (zero? (system* "gcc" > + "-DOPENMP" > + "-fopenmp" > + "-O3" > + "-finline-functions" > + "-funroll-loops" > + "-Wall" > + "-o" > + "FastTreeMP" > + source > + "-lm"))))) Is there any reason to build the single-threaded version? Maybe it would be better to omit it, and call the multi-threaded version FastTree. What do you think? Thanks, Mark
