GNU bug report logs - #32561
[PATCH] gnu: Add gffcompare.

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From: help-debbugs <at> gnu.org (GNU bug Tracking System)
To: Leo Famulari <leo <at> famulari.name>
Cc: tracker <at> debbugs.gnu.org
Subject: bug#32561: closed ([PATCH] gnu: Add gffcompare.)
Date: Wed, 29 Aug 2018 18:16:02 +0000

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Your message dated Wed, 29 Aug 2018 14:15:16 -0400
with message-id <20180829181516.GB26984 <at> jasmine.lan>
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.

(If you believe you have received this mail in error, please contact
help-debbugs <at> gnu.org.)


-- 
32561: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=32561
GNU Bug Tracking System
Contact help-debbugs <at> gnu.org with problems

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From: pimi <madalinionel.patrascu <at> mdc-berlin.de>
To: <guix-patches <at> gnu.org>
Cc: pimi <madalinionel.patrascu <at> mdc-berlin.de>
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:
+@enumerate
+@item compare and evaluate the accuracy of RNA-Seq transcript assemblers
+(Cufflinks, Stringtie);
+@item collapse (merge) duplicate transcripts from multiple GTF/GFF3 files (e.g.
+resulted from assembly of different samples);
+@item 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).
+@end enumerate")
+      (license
+       (list
+        license:expat                   ;license for gffcompare
+        license:artistic2.0)))))        ;license for gclib
-- 
2.17.1

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From: Leo Famulari <leo <at> famulari.name>
To: pimi <madalinionel.patrascu <at> mdc-berlin.de>
Cc: 32561-done <at> debbugs.gnu.org
Subject: Re: [bug#32561] [PATCH] gnu: Add gffcompare.
Date: Wed, 29 Aug 2018 14:15:16 -0400

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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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