From 847acc3206c34b45cabd4f5ae1465a576d7ef10a Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 29 Mar 2022 13:42:48 +0200
Subject: gnu: pigx-rnaseq: Update to 0.0.20.

* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.20.
[source]: Remove patch.
[inputs]: Add megadepth.
* gnu/packages/patches/pigx-rnaseq-no-citeproc.patch: Remove patch.
* gnu/local.mk (dist_patch_DATA): Remove it.
---
 gnu/local.mk                                       |  1 -
 gnu/packages/bioinformatics.scm                    |  6 ++--
 gnu/packages/patches/pigx-rnaseq-no-citeproc.patch | 33 ----------------------
 3 files changed, 3 insertions(+), 37 deletions(-)
 delete mode 100644 gnu/packages/patches/pigx-rnaseq-no-citeproc.patch

diff --git a/gnu/local.mk b/gnu/local.mk
index 4f60046a5e..3f4f2c187d 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1628,7 +1628,6 @@ 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-rnaseq-no-citeproc.patch		\
   %D%/packages/patches/pigx-sars-cov2-ww-no-citeproc.patch	\
   %D%/packages/patches/pigx-scrnaseq-no-citeproc.patch		\
   %D%/packages/patches/pinball-system-ltdl.patch		\
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index ada5965e5f..c42174e0d6 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10869,7 +10869,7 @@ once.  This package provides tools to perform Drop-seq analyses.")
 (define-public pigx-rnaseq
   (package
     (name "pigx-rnaseq")
-    (version "0.0.19")
+    (version "0.0.20")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/BIMSBbioinfo/pigx_rnaseq/"
@@ -10877,8 +10877,7 @@ once.  This package provides tools to perform Drop-seq analyses.")
                                   "/pigx_rnaseq-" version ".tar.gz"))
               (sha256
                (base32
-                "1ja3bda1appxrzbfy7wp7khy30mm7lic8xbq3gkbpc5bld3as9cm"))
-              (patches (search-patches "pigx-rnaseq-no-citeproc.patch"))))
+                "0bf65qqvlkc77vl7cmmzacq70f0qav4p6nf8pp3x1vdd0nvhr24f"))))
     (build-system gnu-build-system)
     (arguments
      `(#:parallel-tests? #f             ; not supported
@@ -10909,6 +10908,7 @@ once.  This package provides tools to perform Drop-seq analyses.")
            sed
            gzip
            snakemake
+           megadepth
            multiqc
            star-for-pigx
            hisat2
diff --git a/gnu/packages/patches/pigx-rnaseq-no-citeproc.patch b/gnu/packages/patches/pigx-rnaseq-no-citeproc.patch
deleted file mode 100644
index 366ae3890a..0000000000
--- a/gnu/packages/patches/pigx-rnaseq-no-citeproc.patch
+++ /dev/null
@@ -1,33 +0,0 @@
-diff -Naur pigx_rnaseq-0.0.19/configure.ac pigx_rnaseq-0.0.19.patched/configure.ac
---- pigx_rnaseq-0.0.19/configure.ac	2021-07-23 14:01:00.304391428 +0200
-+++ pigx_rnaseq-0.0.19.patched/configure.ac	2021-10-06 13:51:29.512960106 +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([STAR],            [STAR])
- find_or_override_prog([HISAT2],          [hisat2])
- find_or_override_prog([HISAT2_BUILD],    [hisat2-build])
-diff -Naur pigx_rnaseq-0.0.19/Makefile.in pigx_rnaseq-0.0.19.patched/Makefile.in
---- pigx_rnaseq-0.0.19/Makefile.in	2021-08-13 13:40:10.402922844 +0200
-+++ pigx_rnaseq-0.0.19.patched/Makefile.in	2021-10-06 13:51:04.052247524 +0200
-@@ -410,7 +410,6 @@
- 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_rnaseq-0.0.19/pigx-common/common/pigx-runner.in pigx_rnaseq-0.0.19.patched/pigx-common/common/pigx-runner.in
---- pigx_rnaseq-0.0.19/pigx-common/common/pigx-runner.in	2021-08-13 13:27:50.494352532 +0200
-+++ pigx_rnaseq-0.0.19.patched/pigx-common/common/pigx-runner.in	2021-10-06 13:51:38.798220108 +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']
-- 
cgit v1.2.3