02/02: gnu: pigx-sars-cov2-ww: Update to 0.0.5.

[guix-commits]

rekado pushed a commit to branch master
in repository guix.

commit 6d5964e8049b141b447c020e699ecaddc29e28fd
Author: Ricardo Wurmus <rekado@elephly.net>
AuthorDate: Tue Mar 29 13:49:50 2022 +0200

    gnu: pigx-sars-cov2-ww: Update to 0.0.5.
    
    * gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww): Update to 0.0.5.
    [source]: Remove patch.
    [arguments]: Disable tests.
    * gnu/packages/patches/pigx-sars-cov2-ww-no-citeproc.patch: Remove file.
    * gnu/local.mk (dist_patch_DATA): Remove it.
---
 gnu/local.mk                                       |  1 -
 gnu/packages/bioinformatics.scm                    |  8 +++---
 .../patches/pigx-sars-cov2-ww-no-citeproc.patch    | 33 ----------------------
 3 files changed, 4 insertions(+), 38 deletions(-)

diff --git a/gnu/local.mk b/gnu/local.mk
index 3f4f2c187d..a704161abc 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-sars-cov2-ww-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              \
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index c42174e0d6..73b9ee6da8 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -11192,7 +11192,7 @@ based methods.")
 (define-public pigx-sars-cov2-ww
   (package
     (name "pigx-sars-cov2-ww")
-    (version "0.0.4")
+    (version "0.0.5")
     (source (origin
               (method url-fetch)
               (uri (string-append 
"https://github.com/BIMSBbioinfo/pigx_sarscov2_ww/";
@@ -11200,11 +11200,11 @@ based methods.")
                                   "/pigx_sars-cov2-ww-" version ".tar.gz"))
               (sha256
                (base32
-                "0axnmz4d8zgir888mc0cilcq4m3v41xmjmpp3w3444lciwnxydvs"))
-              (patches (search-patches 
"pigx-sars-cov2-ww-no-citeproc.patch"))))
+                "1fkr9gp09zl5n7kdqmy9lrnq28k2z97wg74wgkyfssfyxvmq9cr2"))))
     (build-system gnu-build-system)
     (arguments
-     `(#:phases
+     `(#:tests? #f ;requires huge kraken database
+       #:phases
        (modify-phases %standard-phases
          (add-before 'bootstrap 'autoreconf
            (lambda _
diff --git a/gnu/packages/patches/pigx-sars-cov2-ww-no-citeproc.patch 
b/gnu/packages/patches/pigx-sars-cov2-ww-no-citeproc.patch
deleted file mode 100644
index 3f34bca6b2..0000000000
--- a/gnu/packages/patches/pigx-sars-cov2-ww-no-citeproc.patch
+++ /dev/null
@@ -1,33 +0,0 @@
-diff -Naur pigx_sars-cov2-ww-0.0.3/configure.ac 
pigx_sars-cov2-ww-0.0.3.patched/configure.ac
---- pigx_sars-cov2-ww-0.0.3/configure.ac       2021-06-10 10:12:00.552889984 
+0200
-+++ pigx_sars-cov2-ww-0.0.3.patched/configure.ac       2021-10-05 
14:52:32.318695129 +0200
-@@ -50,7 +50,6 @@
- find_or_override_prog([MULTIQC],         [multiqc])
- find_or_override_prog([WGET],            [wget])
- find_or_override_prog([PANDOC],          [pandoc])
--find_or_override_prog([PANDOC_CITEPROC], [pandoc-citeproc])
- 
- AC_ARG_ENABLE([r-packages-check],
-   AS_HELP_STRING([--disable-r-packages-check], [Do not check any R 
packages.]),
-diff -Naur pigx_sars-cov2-ww-0.0.3/Makefile.in 
pigx_sars-cov2-ww-0.0.3.patched/Makefile.in
---- pigx_sars-cov2-ww-0.0.3/Makefile.in        2021-08-05 16:33:59.164123383 
+0200
-+++ pigx_sars-cov2-ww-0.0.3.patched/Makefile.in        2021-10-05 
14:52:41.272958547 +0200
-@@ -402,7 +402,6 @@
- PACKAGE_URL = @PACKAGE_URL@
- PACKAGE_VERSION = @PACKAGE_VERSION@
- PANDOC = @PANDOC@
--PANDOC_CITEPROC = @PANDOC_CITEPROC@
- PATH_SEPARATOR = @PATH_SEPARATOR@
- PRINSEQ = @PRINSEQ@
- PYTHON = @PYTHON@
-diff -Naur pigx_sars-cov2-ww-0.0.3/pigx-common/common/pigx-runner.in 
pigx_sars-cov2-ww-0.0.3.patched/pigx-common/common/pigx-runner.in
---- pigx_sars-cov2-ww-0.0.3/pigx-common/common/pigx-runner.in  2021-07-30 
11:10:17.913115902 +0200
-+++ pigx_sars-cov2-ww-0.0.3.patched/pigx-common/common/pigx-runner.in  
2021-10-05 14:52:23.602438714 +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']