diff --git a/gnu/local.mk b/gnu/local.mk index b9d62a3f0f..c7625a7679 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1628,7 +1628,6 @@ dist_patch_DATA = \ %D%/packages/patches/picard-fix-id3-rename-test.patch \ %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/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 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']