gnu: pigx-chipseq: Update to 0.1.0.

* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.1.0.
[source]: Remove patch.
[arguments]: Remove 'autoreconf phase.
[native-inputs]: Remove autoconf and automake.
* gnu/packages/patches/pigx-chipseq-no-citeproc.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove patch.

gnu/local.mk

@@ -1629,7 +1629,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/picprog-non-intel-support.patch		\
   %D%/packages/patches/pidgin-add-search-path.patch		\
   %D%/packages/patches/pigx-bsseq-no-citeproc.patch		\
-  %D%/packages/patches/pigx-chipseq-no-citeproc.patch		\
   %D%/packages/patches/pinball-system-ltdl.patch		\
   %D%/packages/patches/pingus-boost-headers.patch		\
   %D%/packages/patches/pingus-sdl-libs-config.patch		\

gnu/packages/bioinformatics.scm

@@ -10526,7 +10526,7 @@ expression report comparing samples in an easily configurable manner.")
 (define-public pigx-chipseq
   (package
     (name "pigx-chipseq")
-    (version "0.0.53")
+    (version "0.1.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/BIMSBbioinfo/pigx_chipseq/"
@@ -10534,25 +10534,12 @@ expression report comparing samples in an easily configurable manner.")
                                   "/pigx_chipseq-" version ".tar.gz"))
               (sha256
                (base32
-                "0c6npx35sszycf059w1x1k4k9hq1qqxny0i4p57q1188czr4561h"))
+                "008n6drj9q5av86xihxlj4py2c9p3c5z5ld89c3bksrp77zxiy67"))))
-              (patches (search-patches "pigx-chipseq-no-citeproc.patch"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f ; parts of the tests rely on access to the network
        #:phases
        (modify-phases %standard-phases
-         (add-before 'bootstrap 'autoreconf
-           (lambda _
-             ;; This was fixed in commit
-             ;; 0b1c9f7f2e4d0ff601f1de95ab8b2953f4d5dbc7, but there is no
-             ;; release with this fix.
-             (call-with-output-file "VERSION"
-               (lambda (port) (display ,version port)))
-             ;; See https://github.com/BIMSBbioinfo/pigx_chipseq/issues/176
-             (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")))))))
@@ -10606,7 +10593,7 @@ expression report comparing samples in an easily configurable manner.")
            bedtools
            kentutils))
     (native-inputs
-     (list autoconf automake python-pytest))
+     (list python-pytest))
     (home-page "https://bioinformatics.mdc-berlin.de/pigx/")
     (synopsis "Analysis pipeline for ChIP sequencing experiments")
     (description "PiGX ChIPseq is an analysis pipeline for preprocessing, peak

gnu/packages/patches/pigx-chipseq-no-citeproc.patch

@@ -1,33 +0,0 @@
-diff -Naur pigx_chipseq-0.0.53/configure.ac pigx_chipseq-0.0.53.patched/configure.ac
---- pigx_chipseq-0.0.53/configure.ac	2021-09-28 11:14:12.000000000 +0200
-+++ pigx_chipseq-0.0.53.patched/configure.ac	2021-10-07 14:48:53.034054327 +0200
-@@ -52,7 +52,6 @@
- find_or_override_prog([MACS2],           [macs2])
- 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([BOWTIE2],         [bowtie2])
- find_or_override_prog([BOWTIE2_BUILD],   [bowtie2-build])
-diff -Naur pigx_chipseq-0.0.53/Makefile.in pigx_chipseq-0.0.53.patched/Makefile.in
---- pigx_chipseq-0.0.53/Makefile.in	2021-09-28 11:55:05.000000000 +0200
-+++ pigx_chipseq-0.0.53.patched/Makefile.in	2021-10-07 14:48:37.195577143 +0200
-@@ -407,7 +407,6 @@
- PACKAGE_URL = @PACKAGE_URL@
- PACKAGE_VERSION = @PACKAGE_VERSION@
- PANDOC = @PANDOC@
--PANDOC_CITEPROC = @PANDOC_CITEPROC@
- PATH_SEPARATOR = @PATH_SEPARATOR@
- PERL = @PERL@
- PYTHON = @PYTHON@
-diff -Naur pigx_chipseq-0.0.53/pigx-common/common/pigx-runner.in pigx_chipseq-0.0.53.patched/pigx-common/common/pigx-runner.in
---- pigx_chipseq-0.0.53/pigx-common/common/pigx-runner.in	2021-09-27 18:16:42.000000000 +0200
-+++ pigx_chipseq-0.0.53.patched/pigx-common/common/pigx-runner.in	2021-10-07 14:48:44.200788218 +0200
-@@ -379,7 +379,6 @@
-     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']