[debbugs-tracker] bug#32561: closed ([PATCH] gnu: Add gffcompare.)

[GNU bug Tracking System]

Your message dated Wed, 29 Aug 2018 14:15:16 -0400
with message-id <address@hidden>
and subject line Re: [bug#32561] [PATCH] gnu: Add gffcompare.
has caused the debbugs.gnu.org bug report #32561,
regarding [PATCH] gnu: Add gffcompare.
to be marked as done.

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-- 
32561: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=32561
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> --- Begin Message ---
>
>
>
> Subject: 
>
> [PATCH] gnu: Add gffcompare.
>
>
>
>
> Date: 
>
> Tue, 28 Aug 2018 22:26:13 +0200
>
>
>
>
> gnu/packages/bioinformatics.scm (gffcompare): New variable.
> ---
>  gnu/packages/bioinformatics.scm | 64 +++++++++++++++++++++++++++++++++
>  1 file changed, 64 insertions(+)
>
> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
> index cb3c4bc1f..99f92ad66 100644
> --- a/gnu/packages/bioinformatics.scm
> +++ b/gnu/packages/bioinformatics.scm
> @@ -13458,3 +13458,67 @@ conversions, region filtering, FASTA sequence 
> extraction and more.")
>  spliced (back-spliced) sequencing reads, indicative of circular RNA (circRNA)
>  in RNA-seq data.")
>        (license license:gpl3))))
> +
> +(define-public gffcompare
> +  (let ((commit "be56ef4349ea3966c12c6397f85e49e047361c41")
> +        (revision "1"))
> +    (package
> +      (name "gffcompare")
> +      (version (git-version "0.10.15" revision commit))
> +      (source
> +       (origin
> +         (method git-fetch)
> +         (uri (git-reference
> +               (url "https://github.com/gpertea/gffcompare/";)
> +               (commit commit)))
> +         (file-name (git-file-name name version))
> +         (sha256
> +          (base32 "0cp5qpxdhw4mxpya5dld8wi3jk00zyklm6rcri426wydinrnfmkg"))))
> +      (build-system gnu-build-system)
> +      (arguments
> +       `(#:tests? #f                    ; no check target
> +                  #:phases
> +                  (modify-phases %standard-phases
> +                    (delete 'configure)
> +                    (add-before 'build 'copy-gclib-source
> +                      (lambda* (#:key inputs #:allow-other-keys)
> +                        (mkdir "../gclib")
> +                        (copy-recursively
> +                         (assoc-ref inputs "gclib-source") "../gclib")
> +                        #t))
> +                    (replace 'install
> +                      (lambda* (#:key outputs #:allow-other-keys)
> +                        (let ((bin (string-append (assoc-ref outputs "out") 
> "/bin")))
> +                          (mkdir-p bin)
> +                          (install-file "gffcompare" bin)
> +                          #t))))))
> +      (native-inputs
> +       `(("gclib-source"
> +          ,(let ((commit "54917d0849c1e83cfb057b5f712e5cb6a35d948f")
> +                 (revision "1")
> +                 (name "gclib")
> +                 (version (git-version "0.10.3" revision commit)))
> +             (origin
> +               (method git-fetch)
> +               (uri (git-reference
> +                     (url "https://github.com/gpertea/gclib/";)
> +                     (commit commit)))
> +               (file-name (git-file-name name version))
> +               (sha256
> +                (base32 
> "0b51lc0b8syrv7186fd7n8f15rwnf264qgfmm2palrwks1px24mr")))))))
> +      (home-page "https://github.com/gpertea/gffcompare/";)
> +      (synopsis "Tool for comparing or classifing transcripts of RNA-Seq")
> +      (description
> +       "@code{gffcompare} is a tool that can:
> address@hidden
> address@hidden compare and evaluate the accuracy of RNA-Seq transcript 
> assemblers
> +(Cufflinks, Stringtie);
> address@hidden collapse (merge) duplicate transcripts from multiple GTF/GFF3 
> files (e.g.
> +resulted from assembly of different samples);
> address@hidden classify transcripts from one or multiple GTF/GFF3 files as they 
> relate to
> +reference transcripts provided in a annotation file (also in GTF/GFF3 format).
> address@hidden enumerate")
> +      (license
> +       (list
> +        license:expat                   ;license for gffcompare
> +        license:artistic2.0)))))        ;license for gclib
> -- 
> 2.17.1
>
>
>
>
> --- End Message ---

--- Begin Message --- Subject: Re: [bug#32561] [PATCH] gnu: Add gffcompare. Date: Wed, 29 Aug 2018 14:15:16 -0400 User-agent: Mutt/1.10.1 (2018-07-13)

On Tue, Aug 28, 2018 at 10:26:13PM +0200, pimi wrote:
> gnu/packages/bioinformatics.scm (gffcompare): New variable.

Thanks!

> +      (arguments
> +       `(#:tests? #f                    ; no check target
> +                  #:phases
> +                  (modify-phases %standard-phases
> +                    (delete 'configure)
> +                    (add-before 'build 'copy-gclib-source
> +                      (lambda* (#:key inputs #:allow-other-keys)
> +                        (mkdir "../gclib")
> +                        (copy-recursively
> +                         (assoc-ref inputs "gclib-source") "../gclib")
> +                        #t))
> +                    (replace 'install
> +                      (lambda* (#:key outputs #:allow-other-keys)
> +                        (let ((bin (string-append (assoc-ref outputs "out") 
> "/bin")))
> +                          (mkdir-p bin)
> +                          (install-file "gffcompare" bin)
> +                          #t))))))

I moved the #:phases block over to line up with #:tests?...

> +      (native-inputs
> +       `(("gclib-source"
> +          ,(let ((commit "54917d0849c1e83cfb057b5f712e5cb6a35d948f")

... and added a comment about this, and pushed as
4f9355c3606ecbe83dce78e6d01fa974d912bd4a

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