Ben Woodcroft <b.woodcr...@uq.edu.au> writes:
> From 3f253f059edee5ee2fdb116e310ab210646acf40 Mon Sep 17 00:00:00 2001
> From: Ben Woodcroft <donttrust...@gmail.com>
> Date: Sat, 11 Jul 2015 16:49:30 +1000
> Subject: [PATCH] gnu: Add metabat.
>
> * gnu/packages/bioinformatics.scm (metabat): New variable.
> ---
> gnu/packages/bioinformatics.scm | 72
> +++++++++++++++++++++++++++++++++++++++++
> 1 file changed, 72 insertions(+)
>
> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
> index a28832d..a349d39 100644
> --- a/gnu/packages/bioinformatics.scm
> +++ b/gnu/packages/bioinformatics.scm
> @@ -1394,6 +1394,78 @@ resolution of binding sites through combining the
> information of both
> sequencing tag position and orientation.")
> (license license:bsd-3)))
>
> +(define-public metabat
> + (package
> + (name "metabat")
> + (version "0.26.1")
> + (source (origin
> + (method url-fetch)
> + (uri (string-append
> + "https://bitbucket.org/berkeleylab/metabat/get/";
> + version ".tar.bz2"))
> + (file-name (string-append name "-" version ".tar.gz"))
The file-name should end with ".bz2", not ".gz".
> + (sha256
> + (base32
> + "0vgrhbaxg4dkxyax2kbigak7w0arhqvw0szwp6gd9wmyilc44kfa"))))
> + (build-system gnu-build-system)
> + (arguments
> + `(#:tests? #f ; tests run as part of build phase
It's a nitpick, but in this case it might be marginally nicer to just
delete the 'check' phase, and to put a comment above the (delete 'check)
and (delete 'install) explaining that the tests and install are both
done as part of the build phase.
> + #:phases
> + (modify-phases %standard-phases
> + (replace 'configure
> + (lambda* _
> + (substitute* "SConstruct" ; Do not distribute README
> + (("env.Install.idir_prefix, 'README.md'.") ""))
"env\\.Install\\(idir_prefix, 'README\\.md'\\)"
> + #t))
> + (replace 'build
> + (lambda* (#:key inputs outputs #:allow-other-keys)
> + (substitute* "SConstruct"
> + (("/include/bam/bam.h")
> + "/include/samtools/bam.h"))
> + (substitute* "src/BamUtils.h"
> + (("#include .bam/bam.h.")
> + "#include \"samtools/bam.h\""))
> + (substitute* "src/BamUtils.h"
> + (("#include .bam/sam.h.")
> + "#include \"samtools/sam.h\""))
> + (substitute* "src/KseqReader.h"
> + (("#include \"bam/kseq.h\"")
> + "#include \"samtools/kseq.h\""))
Please move these to a different phase, maybe named 'fix-includes'.
Also, please use \\. in the patterns to match a literal period, put ^ to
anchor them to the start of a line, and use \" to match the start+end
quotes in the includes. Finally, please combine the two substitute*
calls for "src/BamUtils.h" into a single call. So, maybe something like
this: (untested)
--8<---------------cut here---------------start------------->8---
(add-after 'unpack 'fix-includes
(lambda _
(substitute* "SConstruct"
(("/include/bam/bam\\.h")
"/include/samtools/bam.h"))
(substitute* "src/BamUtils.h"
(("^#include \"bam/bam\\.h\"")
"#include \"samtools/bam.h\"")
(("^#include \"bam/sam\\.h\"")
"#include \"samtools/sam.h\""))
(substitute* "src/KseqReader.h"
(("^#include \"bam/kseq\\.h\"")
"#include \"samtools/kseq.h\""))
#t))
--8<---------------cut here---------------end--------------->8---
> + (delete 'install))))
> + (inputs
> + `(("zlib" ,zlib)
> + ("perl" ,perl)
> + ("samtools" ,samtools)
> + ("htslib" ,htslib)))
> + (native-inputs
> + `(("boost" ,boost)
boost should be in 'inputs', not 'native-inputs'.
> + ("scons" ,scons)))
> + (home-page "https://bitbucket.org/berkeleylab/metabat";)
> + (synopsis "Reconstruction of single genomes from complex microbial
> communities")
Please move the string to the next line, to avoid running over 80
columns.
> + (description
> + "Grouping large genomic fragments assembled from shotgun metagenomic
> +sequences to deconvolute complex microbial communities, or metagenome
> binning,
> +enables the study of individual organisms and their interactions. MetaBAT is
> +an automated metagenome binning software, which integrates empirical
> +probabilistic distances of genome abundance and tetranucleotide frequency.")
> + (license (license:non-copyleft "file://license.txt"
> + "See LICENSE in the distribution."))))
s/LICENSE/license.txt/
Can you send an updated patch?
Thanks,
Mark
