01/03: gnu: pigx-scrnaseq: Update to 1.1.8.

[guix-commits]

rekado pushed a commit to branch master
in repository guix.

commit 5d1c9fcdcf81bb95516f2d44e293c760300c9589
Author: Ricardo Wurmus <rekado@elephly.net>
AuthorDate: Tue Apr 5 17:26:00 2022 +0200

    gnu: pigx-scrnaseq: Update to 1.1.8.
    
    * gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 1.1.8.
    [patches]: Remove.
    [native-inputs]: Remove.
    * gnu/packages/patches/pigx-scrnaseq-no-citeproc.patch: Remove file.
    * gnu/local.mk (dist_patch_DATA): Remove it.
---
 gnu/local.mk                                       |  1 -
 gnu/packages/bioinformatics.scm                    | 12 ++------
 .../patches/pigx-scrnaseq-no-citeproc.patch        | 33 ----------------------
 3 files changed, 3 insertions(+), 43 deletions(-)

diff --git a/gnu/local.mk b/gnu/local.mk
index f5e2702031..420aa91d86 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1627,7 +1627,6 @@ dist_patch_DATA =                                         
\
   %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/pigx-scrnaseq-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            \
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index eed7e54f7f..3ad8800fdb 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -11132,7 +11132,7 @@ methylation and segmentation.")
 (define-public pigx-scrnaseq
   (package
     (name "pigx-scrnaseq")
-    (version "1.1.7")
+    (version "1.1.8")
     (source (origin
               (method url-fetch)
               (uri (string-append 
"https://github.com/BIMSBbioinfo/pigx_scrnaseq/";
@@ -11140,20 +11140,14 @@ methylation and segmentation.")
                                   "/pigx_scrnaseq-" version ".tar.gz"))
               (sha256
                (base32
-                "1h5mcxzwj3cidlkvy9ly5wmi48vwfsjf8dxjfirknqxr9a92hwlx"))
-              (patches (search-patches "pigx-scrnaseq-no-citeproc.patch"))))
+                "1lc42hl8mz95kilh0z39s3wnv092mhm6vl2i394n0yfvdzk4f885"))))
     (build-system gnu-build-system)
     (arguments
-     `(#:phases
+     '(#:phases
        (modify-phases %standard-phases
-         (add-before 'bootstrap 'autoreconf
-           (lambda _
-             (invoke "autoreconf" "-vif")))
          (add-before 'configure 'set-PYTHONPATH
            (lambda _
              (setenv "PYTHONPATH" (getenv "GUIX_PYTHONPATH")))))))
-    (native-inputs
-     (list automake autoconf))
     (inputs
      `(("coreutils" ,coreutils)
        ("perl" ,perl)
diff --git a/gnu/packages/patches/pigx-scrnaseq-no-citeproc.patch 
b/gnu/packages/patches/pigx-scrnaseq-no-citeproc.patch
deleted file mode 100644
index 4cce33fb01..0000000000
--- a/gnu/packages/patches/pigx-scrnaseq-no-citeproc.patch
+++ /dev/null
@@ -1,33 +0,0 @@
-diff -Naur pigx_scrnaseq-1.1.7/configure.ac 
pigx_scrnaseq-1.1.7.patched/configure.ac
---- pigx_scrnaseq-1.1.7/configure.ac   2020-03-17 14:37:46.000000000 +0100
-+++ pigx_scrnaseq-1.1.7.patched/configure.ac   2021-10-06 13:55:49.779271317 
+0200
-@@ -43,7 +43,6 @@
- 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([STAR],            [STAR])
- find_or_override_prog([SAMTOOLS],        [samtools])
-diff -Naur pigx_scrnaseq-1.1.7/Makefile.in 
pigx_scrnaseq-1.1.7.patched/Makefile.in
---- pigx_scrnaseq-1.1.7/Makefile.in    2020-11-30 16:55:48.000000000 +0100
-+++ pigx_scrnaseq-1.1.7.patched/Makefile.in    2021-10-06 13:55:52.224340194 
+0200
-@@ -395,7 +395,6 @@
- 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_scrnaseq-1.1.7/pigx-scrnaseq.in 
pigx_scrnaseq-1.1.7.patched/pigx-scrnaseq.in
---- pigx_scrnaseq-1.1.7/pigx-scrnaseq.in       2020-11-30 16:08:55.000000000 
+0100
-+++ pigx_scrnaseq-1.1.7.patched/pigx-scrnaseq.in       2021-10-06 
13:55:47.889218079 +0200
-@@ -274,7 +274,6 @@
-     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']