Patchwork gnu: Add bamm.

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Submitter Ben Woodcroft
Date Aug. 13, 2016, 11:19 a.m.
Message ID <20160813111939.31610-2-donttrustben@gmail.com>
Download mbox | patch
Permalink /patch/14532/
State New
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Comments

Ben Woodcroft - Aug. 13, 2016, 11:19 a.m.
* gnu/packages/bioinformatics.scm (bamm): New variable.
---
 gnu/packages/bioinformatics.scm | 94 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 94 insertions(+)
Alex Kost - Aug. 13, 2016, 2:46 p.m.
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")
Ben Woodcroft - Aug. 14, 2016, 4:57 a.m.
On 14/08/16 00:46, Alex Kost wrote:

[..]

Thanks Alex, correct on all counts. I pushed as 'a12ba6e'.

ben

Patch

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")