From 5a1b2467361edcf8f2f9c7399658b4e136e979d4 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 25 Apr 2023 19:45:13 +0200
Subject: gnu: adapterremoval: Update to 2.3.3.

* gnu/packages/bioinformatics.scm (adapterremoval): Update to 2.3.3.
[arguments]: Simplify.
[inputs]: Reformat.
---
 gnu/packages/bioinformatics.scm | 20 ++++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 1dbacdbd8d..81e6416abe 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -16232,7 +16232,7 @@ tools which build on STAR, Arriba does not require to reduce the
 (define-public adapterremoval
   (package
     (name "adapterremoval")
-    (version "2.3.0")
+    (version "2.3.3")
     (source
      (origin
        (method git-fetch)
@@ -16242,18 +16242,18 @@ tools which build on STAR, Arriba does not require to reduce the
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "1nf3ki5pfzalhrx2fr1y6pfqfi133yj2m7q4fj9irf5fb94bapwr"))))
+         "0wyr182667wqdmzhwwa6f7dddr8kk0scgzb8lsm23wim544mvn6i"))))
     (build-system gnu-build-system)
     (arguments
-     `(#:make-flags
-       ,#~(list "COLOR_BUILD=no"
-                (string-append "PREFIX=" #$output))
-       #:test-target "test"
-       #:phases
-       (modify-phases %standard-phases
+     (list
+      #:make-flags
+      #~(list "COLOR_BUILD=no"
+              (string-append "PREFIX=" #$output))
+      #:test-target "test"
+      #:phases
+      '(modify-phases %standard-phases
          (delete 'configure))))
-    (inputs
-     (list zlib))
+    (inputs (list zlib))
     (home-page "https://adapterremoval.readthedocs.io/")
     (synopsis "Rapid sequence adapter trimming, identification, and read merging")
     (description
-- 
cgit v1.2.3

option>
</select>
<input class='txt' type='search' size='10' name='q' value=''/>
<input type='submit' value='search'/>
</form>
</td></tr></table>
<div class='path'>path: <a href='/guix/log/?id=fe9d09dca4674c1a309eefe5fbf324c61ba975d1'>root</a>/<a href='/guix/log/gnu?id=fe9d09dca4674c1a309eefe5fbf324c61ba975d1'>gnu</a>/<a href='/guix/log/gnu/system.scm?id=fe9d09dca4674c1a309eefe5fbf324c61ba975d1'>system.scm</a></div><div class='content'><table class='list nowrap'><tr class='nohover'><th class='left'>Age</th><th class='left'>Commit message (<a href='/guix/log/gnu/system.scm?id=fe9d09dca4674c1a309eefe5fbf324c61ba975d1&amp;showmsg=1'>Expand</a>)</th><th class='left'>Author</th></tr>
<tr><td><span title='2024-08-11 02:00:00 +0200'>2024-08-11</span></td><td><a href='/guix/commit/gnu/system.scm?id=4e58dfee6c7456d1e662f66041b8a157efe8710a'>system: Add privileged-programs to &lt;operating-system&gt;.</a><span class='msg-avail'>...<span class='msg-tooltip'>* gnu/system.scm (&lt;operating-system&gt;): Add new privileged-programs
field, that defaults to…
(%default-privileged-programs): …this new variable, renamed from…
(%setuid-programs): …this, which is now defined as the empty list.
* doc/guix.texi (Setuid Programs): Rename this…
(Privileged Programs): …to this.  Adjust all refs.  Update all mentions
of ‘setuid’ (whether in prose, variable names, or code samples) to use
the new ‘privilege[d]’ terminology instead.
(operating-system Reference, X Window, Invoking guix system)
(Service Reference): Adjust likewise.
</span></span></td><td>Tobias Geerinckx-Rice</td></tr>
<tr><td><span title='2024-08-11 02:00:00 +0200'>2024-08-11</span></td><td><a href='/guix/commit/gnu/system.scm?id=beb37ea4ad9999c28cfb60aca5d021851f9a1176'>system: Use privileged-program-service-type by default.</a><span class='msg-avail'>...<span class='msg-tooltip'>* gnu/system.scm (operating-system-default-essential-services)
(hurd-default-essential-services): Substitute
privileged-program-service-type for setuid-program-service-type.
</span></span></td><td>Tobias Geerinckx-Rice</td></tr>
<tr><td><span title='2024-08-11 02:00:00 +0200'>2024-08-11</span></td><td><a href='/guix/commit/gnu/system.scm?id=e364d1a494140c26f95a90176b3216428bbaf944'>system: Use /run/privileged/bin in search paths.</a><span class='msg-avail'>...<span class='msg-tooltip'>* gnu/system.scm (operating-system-etc-service):
Substitute /run/privileged/bin for deprecated /run/setuid-programs.
</span></span></td><td>Tobias Geerinckx-Rice</td></tr>
<tr><td><span title='2024-08-11 02:00:00 +0200'>2024-08-11</span></td><td><a href='/guix/commit/gnu/system.scm?id=0dffb851e0feced94742ad024f245b925c503fa2'>system: Disallow file-like setuid-programs.</a><span class='msg-avail'>...<span class='msg-tooltip'>It has been a warning for well over a year now.  Now, with
privileged-programs coming, don't let's support nested deprecation
hacks.

* gnu/system.scm (&lt;operating-system&gt;):
Don't ‘sanitize’ the setuid-programs field.
(ensure-setuid-program-list): Delete syntax.
(%ensure-setuid-program-list): Delete variable.
</span></span></td><td>Tobias Geerinckx-Rice</td></tr>