[debbugs-tracker] bug#32984: closed ([PATCH] gnu: Add filtlong.)

[GNU bug Tracking System]

Your message dated Mon, 08 Oct 2018 18:32:06 +0200
with message-id <address@hidden>
and subject line Re: [bug#32984] [PATCH] gnu: Add filtlong.
has caused the debbugs.gnu.org bug report #32984,
regarding [PATCH] gnu: Add filtlong.
to be marked as done.

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-- 
32984: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=32984
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> --- Begin Message ---
>
>
>
> Subject: 
>
> [PATCH] gnu: Add filtlong.
>
>
>
>
> Date: 
>
> Mon, 8 Oct 2018 11:17:41 +0200
>
>
>
>
> * gnu/packages/bioinformatics.scm (filtlong): New variable.
> ---
>  gnu/packages/bioinformatics.scm | 63 +++++++++++++++++++++++++++++++++
>  1 file changed, 63 insertions(+)
>
> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
> index ab9dc185a..43cdf811e 100644
> --- a/gnu/packages/bioinformatics.scm
> +++ b/gnu/packages/bioinformatics.scm
> @@ -14057,3 +14057,66 @@ absolute GSEA.")
>      (description "Ngless is a domain-specific language for
>  @dfn{next-generation sequencing} (NGS) data processing.")
>      (license license:expat)))
> +
> +(define-public filtlong
> +  ;; The recommended way to install is to clone the git repository
> +  ;; https://github.com/rrwick/Filtlong#installation
> +  ;; and the lastest release is more than nine months old
> +  (let ((commit "d1bb46dfe8bc7efe6257b5ce222c04bfe8aedaab")
> +        (revision "1"))
> +    (package
> +      (name "filtlong")
> +      (version (git-version "0.2.0" revision commit))
> +      (source
> +       (origin
> +         (method git-fetch)
> +         (uri (git-reference
> +               (url "https://github.com/rrwick/Filtlong.git";)
> +               (commit commit)))
> +         (file-name (git-file-name name version))
> +         (sha256
> +          (base32 "1xr92r820x8qlkcr3b57iw223yq8vjgyi42jr79w2xgw47qzr575"))))
> +      ;;(properties `((upstream-name . "Filtlong")))
> +      (build-system gnu-build-system)
> +      (arguments
> +       `(#:tests? #f                    ; no check target
> +         #:phases
> +         (modify-phases %standard-phases
> +           (delete 'configure)
> +           (replace 'install
> +             (lambda* (#:key outputs #:allow-other-keys)
> +               (let* ((out (assoc-ref outputs "out"))
> +                      (bin (string-append out "/bin"))
> +                      (scripts (string-append out "/scripts")))
> +                 (mkdir-p bin)
> +                 (mkdir-p scripts)
> +                 (install-file "bin/filtlong" bin)
> +                 (install-file "scripts/histogram.py" scripts)
> +                 (install-file "scripts/read_info_histograms.sh" scripts))
> +               #t))
> +           (add-after 'install 'wrap-program
> +             (lambda* (#:key inputs outputs #:allow-other-keys)
> +               (let* ((out (assoc-ref outputs "out"))
> +                      (path (getenv "PYTHONPATH")))
> +                 ;;(wrap-program (string-apend scripts 
> "scripts/read_info_histograms.sh")
> +                 (wrap-program (string-append out "/scripts/histogram.py")
> +                   `("PYTHONPATH" ":" prefix (,path))))
> +               #t))
> +           (add-before 'check 'patch-tests
> +             (lambda _
> +               (substitute* "scripts/read_info_histograms.sh"
> +                 (("awk") (which "gawk")))
> +               #t)))))
> +      (inputs
> +       `(("gawk" ,gawk)                 ;for read_info_histograms.sh
> +         ("python" ,python-2)           ; required for histogram.py
> +         ("zlib" ,zlib)))
> +      (home-page "https://github.com/rrwick/Filtlong/";)
> +      (synopsis "Tool for quality filtering of Nanopore and PacBio data")
> +      (description
> +       "The @code{filtlong} package is a tool for filtering long reads by 
> quality.
> +It can take a set of long reads and produce a smaller, better subset.  It uses
> +both read length (longer is better) and read identity (higher is better) when
> +choosing which reads pass the filter.")
> +      (license (list license:gpl3       ;filtlong
> +                     license:asl2.0))))) ;histogram.py
> -- 
> 2.17.1
>
>
>
>
> --- End Message ---
> --- Begin Message ---
>
>
>
> Subject: 
>
> Re: [bug#32984] [PATCH] gnu: Add filtlong.
>
>
>
>
> Date: 
>
> Mon, 08 Oct 2018 18:32:06 +0200
>
>
>
>
> User-agent: 
>
> Gnus/5.13 (Gnus v5.13) Emacs/26.1 (gnu/linux)
>
>
>
>
> Hello,
>
> pimi <address@hidden> skribis:
>
> > * gnu/packages/bioinformatics.scm (filtlong): New variable.
>
> Applied with the changes below; let me know if anything is amiss.
>
> Thanks!
>
> Ludo’.
>
> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
> index 43cdf811e..ed713cd14 100644
> --- a/gnu/packages/bioinformatics.scm
> +++ b/gnu/packages/bioinformatics.scm
> @@ -14076,7 +14076,6 @@ absolute GSEA.")
>           (file-name (git-file-name name version))
>           (sha256
>            (base32 "1xr92r820x8qlkcr3b57iw223yq8vjgyi42jr79w2xgw47qzr575"))))
> -      ;;(properties `((upstream-name . "Filtlong")))
>        (build-system gnu-build-system)
>        (arguments
>         `(#:tests? #f                    ; no check target
> @@ -14087,9 +14086,7 @@ absolute GSEA.")
>               (lambda* (#:key outputs #:allow-other-keys)
>                 (let* ((out (assoc-ref outputs "out"))
>                        (bin (string-append out "/bin"))
> -                      (scripts (string-append out "/scripts")))
> -                 (mkdir-p bin)
> -                 (mkdir-p scripts)
> +                      (scripts (string-append out "/share/filtlong/scripts")))
>                   (install-file "bin/filtlong" bin)
>                   (install-file "scripts/histogram.py" scripts)
>                   (install-file "scripts/read_info_histograms.sh" scripts))
> @@ -14098,8 +14095,8 @@ absolute GSEA.")
>               (lambda* (#:key inputs outputs #:allow-other-keys)
>                 (let* ((out (assoc-ref outputs "out"))
>                        (path (getenv "PYTHONPATH")))
> -                 ;;(wrap-program (string-apend scripts 
> "scripts/read_info_histograms.sh")
> -                 (wrap-program (string-append out "/scripts/histogram.py")
> +                 (wrap-program (string-append out
> +                                              
> "/share/filtlong/scripts/histogram.py")
>                     `("PYTHONPATH" ":" prefix (,path))))
>                 #t))
>             (add-before 'check 'patch-tests
> @@ -14114,7 +14111,7 @@ absolute GSEA.")
>        (home-page "https://github.com/rrwick/Filtlong/";)
>        (synopsis "Tool for quality filtering of Nanopore and PacBio data")
>        (description
> -       "The @code{filtlong} package is a tool for filtering long reads by 
> quality.
> +       "The Filtlong package is a tool for filtering long reads by quality.
>  It can take a set of long reads and produce a smaller, better subset.  It uses
>  both read length (longer is better) and read identity (higher is better) when
>  choosing which reads pass the filter.")
>
> --- End Message ---