GNU bug report logs - #77331
[PATCH] gnu: Remove variant-tools.

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From: help-debbugs <at> gnu.org (GNU bug Tracking System)
To: Andreas Enge <andreas <at> enge.fr>
Cc: tracker <at> debbugs.gnu.org
Subject: bug#77331: closed ([PATCH] gnu: Remove variant-tools.)
Date: Tue, 29 Apr 2025 09:36:02 +0000

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Your message dated Tue, 29 Apr 2025 11:35:41 +0200
with message-id <aBCdbXujRGxgFBC4 <at> jurong>
and subject line Re: [PATCH] gnu: Remove variant-tools.
has caused the debbugs.gnu.org bug report #77331,
regarding [PATCH] gnu: Remove variant-tools.
to be marked as done.

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


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77331: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=77331
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From: Andreas Enge <andreas <at> enge.fr>
To: guix-patches <at> gnu.org
Cc: rekado <at> elephly.net, Andreas Enge <andreas <at> enge.fr>
Subject: [PATCH] gnu: Remove variant-tools.
Date: Fri, 28 Mar 2025 10:52:48 +0100

* gnu/packages/bioinformatics.scm (variant-tools): Delete variable.

The package does not compile any more and has no dependent packages.
The last release dates from 2020; there is an additional commit in 2022;
the git repository has been archived in 2023.

Change-Id: Idb5df024121c5085f764f179d31ac67cff3fc5c7
---
Yet another package depending on hdf5, which I noticed does not compile
when I tried to update hdf5, but it already does not compile now.
There is a package r-varianttools in bioconductor, but I think they are
not related.

 gnu/packages/bioinformatics.scm | 37 ---------------------------------
 1 file changed, 37 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 473e91bda9..8fd7789028 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -15248,43 +15248,6 @@ (define-public multiqc
 common bioinformatics tools.")
     (license license:gpl3+)))
 
-(define-public variant-tools
-  (package
-    (name "variant-tools")
-    (version "3.1.2")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-             (url "https://github.com/vatlab/varianttools")
-             ;; There is no tag corresponding to version 3.1.2
-             (commit "813ae4a90d25b69abc8a40f4f70441fe09015249")))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32
-         "12ibdmksj7icyqhks4xyvd61bygk4pjmxn618kp6vgk1af01y34g"))))
-    (build-system python-build-system)
-    (inputs
-     (list boost
-           c-blosc
-           gsl
-           hdf5
-           hdf5-blosc
-           python-cython
-           zlib))
-    (propagated-inputs
-     (list python-numpy python-pycurl python-pyzmq python-scipy
-           python-tables))
-    (home-page "https://vatlab.github.io/vat-docs/")
-    (synopsis "Analyze genetic variants from Next-Gen sequencing studies")
-    (description
-     "Variant tools is a tool for the manipulation, annotation,
-selection, simulation, and analysis of variants in the context of next-gen
-sequencing analysis.  Unlike some other tools used for next-gen sequencing
-analysis, variant tools is project based and provides a whole set of tools to
-manipulate and analyze genetic variants.")
-    (license license:gpl3+)))
-
 (define-public r-chromvarmotifs
   (let ((commit "38bed559c1f4770b6c91c80bf3f8ea965da26076")
         (revision "1"))

base-commit: decc863d46274ef53e5ef6b33e00070fd920a6a7
-- 
2.49.0

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From: Andreas Enge <andreas <at> enge.fr>
To: 77331-done <at> debbugs.gnu.org
Cc: rekado <at> elephly.net
Subject: Re: [PATCH] gnu: Remove variant-tools.
Date: Tue, 29 Apr 2025 11:35:41 +0200

Package removed.

Andreas

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