* [PATCH 0/1] Add BamM.
@ 2016-08-13 11:19 Ben Woodcroft
2016-08-13 11:19 ` [PATCH] gnu: Add bamm Ben Woodcroft
0 siblings, 1 reply; 4+ messages in thread
From: Ben Woodcroft @ 2016-08-13 11:19 UTC (permalink / raw)
To: guix-devel
Hi all,
Note that I have some direct involvement in this project so if needed changes
could be implemented in the code itself.
Thanks in advance.
ben
^ permalink raw reply [flat|nested] 4+ messages in thread
* [PATCH] gnu: Add bamm.
2016-08-13 11:19 [PATCH 0/1] Add BamM Ben Woodcroft
@ 2016-08-13 11:19 ` Ben Woodcroft
2016-08-13 14:46 ` Alex Kost
0 siblings, 1 reply; 4+ messages in thread
From: Ben Woodcroft @ 2016-08-13 11:19 UTC (permalink / raw)
To: guix-devel
* gnu/packages/bioinformatics.scm (bamm): New variable.
---
gnu/packages/bioinformatics.scm | 94 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 94 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b206f33..7728118 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -136,6 +136,100 @@ tRNA consensus sequences and RNA structure. It also outputs the secondary
structure of the predicted RNA.")
(license license:gpl2)))
+(define-public bamm
+ (package
+ (name "bamm")
+ (version "1.7.2a")
+ (source (origin
+ (method url-fetch)
+ ;; BamM is not available on pypi.
+ (uri (string-append
+ "https://github.com/Ecogenomics/BamM/archive/v"
+ version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0nb20yml39f8fh0cahpjywsl91irh9yskig549c17xkrkl74czsq"))
+ (modules '((guix build utils)))
+ (snippet
+ `(begin
+ ;; Delete bundled htslib.
+ (delete-file-recursively "c/htslib-1.3.1")
+ #t))))
+ (build-system python-build-system)
+ (arguments
+ `(#:python ,python-2 ; BamM is Python 2 only.
+ ;; Do not use bundled libhts. Do use the bundled libcfu because it has
+ ;; been modified from its original form.
+ #:configure-flags (list
+ "--with-libhts-lib"
+ (string-append (assoc-ref %build-inputs "htslib")
+ "/lib")
+ "--with-libhts-inc"
+ (string-append (assoc-ref %build-inputs "htslib")
+ "/include/htslib"))
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'autogen
+ (lambda _
+ ;; Use autogen so that 'configure' works.
+ (with-directory-excursion "c"
+ (substitute* "autogen.sh"
+ (("/bin/sh") (which "sh")))
+ (setenv "CONFIG_SHELL" (which "sh"))
+ (substitute* "configure"
+ (("/bin/sh") (which "sh")))
+ (zero? (system* "./autogen.sh")))))
+ (delete 'build)
+ ;; Run tests after installation so compilation only happens once.
+ (delete 'check)
+ (add-after 'install 'post-install-check
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (setenv "PATH"
+ (string-append (assoc-ref outputs "out")
+ "/bin:"
+ (getenv "PATH")))
+ (setenv "PYTHONPATH"
+ (string-append
+ (assoc-ref outputs "out")
+ "/lib/python"
+ (string-take (string-take-right
+ (assoc-ref inputs "python") 5) 3)
+ "/site-packages:"
+ (getenv "PYTHONPATH")))
+ (zero? (system* "nosetests"))))
+ (add-after 'install 'wrap-executable
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (path (getenv "PATH")))
+ (wrap-program (string-append out "/bin/bamm")
+ `("PATH" ":" prefix (,path))))
+ #t)))))
+ (native-inputs
+ `(("autoconf" ,autoconf)
+ ("automake" ,automake)
+ ("libtool" ,libtool)
+ ("zlib" ,zlib)
+ ("python-nose" ,python2-nose)
+ ("python-pysam" ,python2-pysam)
+ ("python-setuptools" ,python2-setuptools)))
+ (inputs
+ `(("htslib" ,htslib)
+ ("samtools" ,samtools)
+ ("bwa" ,bwa)
+ ("grep" ,grep)
+ ("sed" ,sed)
+ ("coreutils" ,coreutils)))
+ (propagated-inputs
+ `(("python-numpy" ,python2-numpy)))
+ (home-page "http://ecogenomics.github.io/BamM/")
+ (synopsis "Metagenomics-focused BAM file manipulator")
+ (description
+ "BamM is a C library, wrapped in python, to efficiently generate and
+parse BAM files, specifically for the analysis of metagenomic data. For
+instance, it implements several methods to assess contig-wise read coverage.")
+ (license license:lgpl3+)))
+
(define-public bamtools
(package
(name "bamtools")
--
2.9.1
^ permalink raw reply related [flat|nested] 4+ messages in thread
* Re: [PATCH] gnu: Add bamm.
2016-08-13 11:19 ` [PATCH] gnu: Add bamm Ben Woodcroft
@ 2016-08-13 14:46 ` Alex Kost
2016-08-14 4:57 ` Ben Woodcroft
0 siblings, 1 reply; 4+ messages in thread
From: Alex Kost @ 2016-08-13 14:46 UTC (permalink / raw)
To: Ben Woodcroft; +Cc: guix-devel
Ben Woodcroft (2016-08-13 14:19 +0300) wrote:
> * gnu/packages/bioinformatics.scm (bamm): New variable.
> ---
> gnu/packages/bioinformatics.scm | 94 +++++++++++++++++++++++++++++++++++++++++
> 1 file changed, 94 insertions(+)
>
>
> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
> index b206f33..7728118 100644
> --- a/gnu/packages/bioinformatics.scm
> +++ b/gnu/packages/bioinformatics.scm
> @@ -136,6 +136,100 @@ tRNA consensus sequences and RNA structure. It also outputs the secondary
> structure of the predicted RNA.")
> (license license:gpl2)))
>
> +(define-public bamm
> + (package
> + (name "bamm")
> + (version "1.7.2a")
> + (source (origin
> + (method url-fetch)
> + ;; BamM is not available on pypi.
> + (uri (string-append
> + "https://github.com/Ecogenomics/BamM/archive/v"
> + version ".tar.gz"))
> + (file-name (string-append name "-" version ".tar.gz"))
> + (sha256
> + (base32
> + "0nb20yml39f8fh0cahpjywsl91irh9yskig549c17xkrkl74czsq"))
> + (modules '((guix build utils)))
> + (snippet
> + `(begin
> + ;; Delete bundled htslib.
> + (delete-file-recursively "c/htslib-1.3.1")
> + #t))))
> + (build-system python-build-system)
> + (arguments
> + `(#:python ,python-2 ; BamM is Python 2 only.
> + ;; Do not use bundled libhts. Do use the bundled libcfu because it has
> + ;; been modified from its original form.
> + #:configure-flags (list
> + "--with-libhts-lib"
> + (string-append (assoc-ref %build-inputs "htslib")
> + "/lib")
> + "--with-libhts-inc"
> + (string-append (assoc-ref %build-inputs "htslib")
> + "/include/htslib"))
I would avoid this duplicating of (assoc-ref %build-inputs "htslib"):
(let ((htslib (assoc-ref %build-inputs "htslib")))
(list "--with-libhts-lib" (string-append htslib "/lib")
"--with-libhts-inc" (string-append htslib "/include/htslib")))
> + #:phases
> + (modify-phases %standard-phases
> + (add-after 'unpack 'autogen
> + (lambda _
> + ;; Use autogen so that 'configure' works.
> + (with-directory-excursion "c"
> + (substitute* "autogen.sh"
> + (("/bin/sh") (which "sh")))
> + (setenv "CONFIG_SHELL" (which "sh"))
> + (substitute* "configure"
> + (("/bin/sh") (which "sh")))
> + (zero? (system* "./autogen.sh")))))
and here as well: you call (which "sh") 3 times! I think it's better to
do (let ((sh (which "sh"))) ...)
> + (delete 'build)
> + ;; Run tests after installation so compilation only happens once.
> + (delete 'check)
> + (add-after 'install 'post-install-check
> + (lambda* (#:key inputs outputs #:allow-other-keys)
> + (setenv "PATH"
> + (string-append (assoc-ref outputs "out")
> + "/bin:"
> + (getenv "PATH")))
> + (setenv "PYTHONPATH"
> + (string-append
> + (assoc-ref outputs "out")
> + "/lib/python"
> + (string-take (string-take-right
> + (assoc-ref inputs "python") 5) 3)
> + "/site-packages:"
> + (getenv "PYTHONPATH")))
> + (zero? (system* "nosetests"))))
> + (add-after 'install 'wrap-executable
> + (lambda* (#:key inputs outputs #:allow-other-keys)
'inputs' argument is not needed here
> + (let* ((out (assoc-ref outputs "out"))
> + (path (getenv "PATH")))
> + (wrap-program (string-append out "/bin/bamm")
> + `("PATH" ":" prefix (,path))))
> + #t)))))
> + (native-inputs
> + `(("autoconf" ,autoconf)
> + ("automake" ,automake)
> + ("libtool" ,libtool)
> + ("zlib" ,zlib)
> + ("python-nose" ,python2-nose)
> + ("python-pysam" ,python2-pysam)
> + ("python-setuptools" ,python2-setuptools)))
> + (inputs
> + `(("htslib" ,htslib)
> + ("samtools" ,samtools)
> + ("bwa" ,bwa)
> + ("grep" ,grep)
> + ("sed" ,sed)
> + ("coreutils" ,coreutils)))
> + (propagated-inputs
> + `(("python-numpy" ,python2-numpy)))
> + (home-page "http://ecogenomics.github.io/BamM/")
> + (synopsis "Metagenomics-focused BAM file manipulator")
> + (description
> + "BamM is a C library, wrapped in python, to efficiently generate and
> +parse BAM files, specifically for the analysis of metagenomic data. For
> +instance, it implements several methods to assess contig-wise read coverage.")
> + (license license:lgpl3+)))
> +
> (define-public bamtools
> (package
> (name "bamtools")
--
Alex
^ permalink raw reply [flat|nested] 4+ messages in thread
* Re: [PATCH] gnu: Add bamm.
2016-08-13 14:46 ` Alex Kost
@ 2016-08-14 4:57 ` Ben Woodcroft
0 siblings, 0 replies; 4+ messages in thread
From: Ben Woodcroft @ 2016-08-14 4:57 UTC (permalink / raw)
To: Alex Kost, Ben Woodcroft; +Cc: guix-devel
On 14/08/16 00:46, Alex Kost wrote:
[..]
Thanks Alex, correct on all counts. I pushed as 'a12ba6e'.
ben
^ permalink raw reply [flat|nested] 4+ messages in thread
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2016-08-13 11:19 [PATCH 0/1] Add BamM Ben Woodcroft
2016-08-13 11:19 ` [PATCH] gnu: Add bamm Ben Woodcroft
2016-08-13 14:46 ` Alex Kost
2016-08-14 4:57 ` Ben Woodcroft
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