From 93c97bfffba7ca0126c03967fbe058354e24f84d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 1 Jun 2022 12:41:59 +0200
Subject: gnu: pigx-bsseq: Update to 0.1.7.

* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.1.7.
[source]: Remove patch.
[arguments]: Remove 'autoreconf phase.
[native-inputs]: Remove automake and autoconf.
* gnu/packages/patches/pigx-bsseq-no-citeproc.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove patch.
---
 gnu/packages/bioinformatics.scm                   | 19 +++----------
 gnu/packages/patches/pigx-bsseq-no-citeproc.patch | 33 -----------------------
 2 files changed, 3 insertions(+), 49 deletions(-)
 delete mode 100644 gnu/packages/patches/pigx-bsseq-no-citeproc.patch

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index f2800d3163..92d92e7d02 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10608,7 +10608,7 @@ in an easily configurable manner.")
 (define-public pigx-bsseq
   (package
     (name "pigx-bsseq")
-    (version "0.1.6")
+    (version "0.1.7")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/BIMSBbioinfo/pigx_bsseq/"
@@ -10616,8 +10616,7 @@ in an easily configurable manner.")
                                   "/pigx_bsseq-" version ".tar.gz"))
               (sha256
                (base32
-                "1dipikph0xdr8fp0h1flpafcrg60y4aabljg8fl1v92j3gxdggmw"))
-              (patches (search-patches "pigx-bsseq-no-citeproc.patch"))))
+                "1hfiignq3410dbl6f67vc6zr69abknpcgxixx475dspky2jb5lyn"))))
     (build-system gnu-build-system)
     (arguments
      `(;; TODO: tests currently require 12+GB of RAM.  See
@@ -10625,18 +10624,6 @@ in an easily configurable manner.")
        #:tests? #f
        #:phases
        (modify-phases %standard-phases
-         (add-before 'bootstrap 'autoreconf
-           (lambda _
-             ;; This was fixed in commit
-             ;; d56ac732524da659afbbb0972f7a87fa178ae58e, but there is no
-             ;; release with this fix.
-             (call-with-output-file "VERSION"
-               (lambda (port) (display ,version port)))
-             ;; https://github.com/BIMSBbioinfo/pigx_bsseq/issues/181
-             (substitute* "m4/ax_r_package.m4"
-               (("if\\(is.na\\(packageDescription\\(\"PKG\"\\)\\)\\)")
-                "if(system.file(package=\"PKG\") == \"\")"))
-             (invoke "autoreconf" "-vif")))
          (add-before 'configure 'set-PYTHONPATH
            (lambda _
              (setenv "PYTHONPATH" (getenv "GUIX_PYTHONPATH"))))
@@ -10648,7 +10635,7 @@ in an easily configurable manner.")
                      (search-input-directory inputs
                                              "share/zoneinfo")))))))
     (native-inputs
-     (list tzdata automake autoconf))
+     (list tzdata))
     (inputs
      (list coreutils
            sed
diff --git a/gnu/packages/patches/pigx-bsseq-no-citeproc.patch b/gnu/packages/patches/pigx-bsseq-no-citeproc.patch
deleted file mode 100644
index 882e660fe4..0000000000
--- a/gnu/packages/patches/pigx-bsseq-no-citeproc.patch
+++ /dev/null
@@ -1,33 +0,0 @@
-diff -Naur pigx_bsseq-0.1.5/configure.ac pigx_bsseq-0.1.5.patched/configure.ac
---- pigx_bsseq-0.1.5/configure.ac	2021-06-08 15:28:08.000000000 +0200
-+++ pigx_bsseq-0.1.5.patched/configure.ac	2021-10-05 14:43:56.806529137 +0200
-@@ -38,7 +38,6 @@
- find_or_override_prog([GNUBASH],         [bash])
- find_or_override_prog([SNAKEMAKE],       [snakemake])
- find_or_override_prog([PANDOC],          [pandoc])
--find_or_override_prog([PANDOC_CITEPROC], [pandoc-citeproc])
- find_or_override_prog([FASTQC],          [fastqc])
- find_or_override_prog([MULTIQC],         [multiqc])
- find_or_override_prog([TRIMGALORE],      [trim_galore])
-diff -Naur pigx_bsseq-0.1.5/Makefile.in pigx_bsseq-0.1.5.patched/Makefile.in
---- pigx_bsseq-0.1.5/Makefile.in	2021-06-08 16:17:03.000000000 +0200
-+++ pigx_bsseq-0.1.5.patched/Makefile.in	2021-10-05 14:43:34.635876855 +0200
-@@ -408,7 +408,6 @@
- PACKAGE_URL = @PACKAGE_URL@
- PACKAGE_VERSION = @PACKAGE_VERSION@
- PANDOC = @PANDOC@
--PANDOC_CITEPROC = @PANDOC_CITEPROC@
- PATH_SEPARATOR = @PATH_SEPARATOR@
- PYTHON = @PYTHON@
- PYTHONPATH = @PYTHONPATH@
-diff -Naur pigx_bsseq-0.1.5/pigx-common/common/pigx-runner.in pigx_bsseq-0.1.5.patched/pigx-common/common/pigx-runner.in
---- pigx_bsseq-0.1.5/pigx-common/common/pigx-runner.in	2021-06-08 10:14:29.000000000 +0200
-+++ pigx_bsseq-0.1.5.patched/pigx-common/common/pigx-runner.in	2021-10-05 14:43:44.296161069 +0200
-@@ -375,7 +375,6 @@
-     if path.exists(bin): shutil.rmtree(bin)
-     os.makedirs(bin, exist_ok=True)
-     os.symlink('@PANDOC@', path.join(bin, "pandoc"))
--    os.symlink('@PANDOC_CITEPROC@', path.join(bin, "pandoc-citeproc"))
-     os.symlink('@RSCRIPT@', path.join(bin, "Rscript"))
-     os.environ['PATH'] = path.abspath(bin) + ":" + os.environ['PATH']
-     os.environ['PIGX_PATH'] = path.abspath(bin) + ":" + os.environ['PATH']
-- 
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