[Gsrc-commit] trunk r8621: update bismark to 0.23.1

[Carl Hansen]

------------------------------------------------------------
revno: 8621
revision-id: carlhansen1234@gmail.com-20221004171836-t6dj6o4k5deaf839
parent: carlhansen1234@gmail.com-20221004162237-8ype3cixk5eeijrw
committer: carlhansen1234@gmail.com
branch nick: trunk
timestamp: Tue 2022-10-04 10:18:36 -0700
message:
  update bismark to 0.23.1
modified:
  pkg/bio/bismark/Makefile       makefile-20160617195624-kwz1a09vkg4le6fu-77
  pkg/bio/bismark/sha256sums     sha256sums-20160617195624-kwz1a09vkg4le6fu-78

=== modified file 'pkg/bio/bismark/Makefile'
--- a/pkg/bio/bismark/Makefile  2021-05-01 05:29:48 +0000
+++ b/pkg/bio/bismark/Makefile  2022-10-04 17:18:36 +0000
@@ -16,7 +16,7 @@
 
 NAME = Bismark
 GARNAME = bismark
-GARVERSION = 0.22.3
+GARVERSION = 0.23.1
 HOME_URL = http://www.bioinformatics.babraham.ac.uk/projects/bismark/
 DESCRIPTION = A bisulfite read mapper and methylation caller
 define BLURB
@@ -27,15 +27,15 @@
 CITE =
 
 ######################################################################
-# 
http://www.bioinformatics.babraham.ac.uk/projects/bismark/bismark_v0.19.1.tar.gz
-
-MASTER_SITES = http://www.bioinformatics.babraham.ac.uk/
-MASTER_SUBDIR = projects/$(GARNAME)/
-DISTNAME = $(GARNAME)_v$(GARVERSION)
-DISTFILES = $(DISTNAME).tar.gz
+# https://github.com/FelixKrueger/Bismark/archive/refs/tags/0.23.1.tar.gz
+# https://github.com/FelixKrueger/Bismark.git
+MASTER_SITES = https://github.com/
+MASTER_SUBDIR = FelixKrueger/Bismark/archive/refs/tags/
+#DISTNAME = $(GARNAME)_v$(GARVERSION)
+DISTFILES = $(GARVERSION).tar.gz
 SIGFILES = 
-INSTALL_SCRIPTS = scripts
-WORKSRC =  $(WORKDIR)/Bismark_v$(GARVERSION)
+INSTALL_SCRIPTS = doscripts
+WORKSRC =  $(WORKDIR)/Bismark-$(GARVERSION)
 
 BUILDDEPS =
 LIBDEPS =
@@ -45,7 +45,7 @@
 include ../../../gar/gar.mk
 include config.mk
 
-install-scripts:
+install-doscripts:
        @printf "[$(OK)install$(OFF)] $(MSG)Installing $(NAME).$(OFF)\n"
        $(INSTALL_BIN) $(WORKSRC)/bismark
        $(INSTALL_BIN) $(WORKSRC)/bismark2bedGraph
@@ -57,3 +57,8 @@
        $(MAKECOOKIE)
 
 # to do install docs...
+#
+# NEEDS 
+#    Bowtie2 or HISAT2
+#    Samtools
+

=== modified file 'pkg/bio/bismark/sha256sums'
--- a/pkg/bio/bismark/sha256sums        2018-06-30 06:30:47 +0000
+++ b/pkg/bio/bismark/sha256sums        2022-10-04 17:18:36 +0000
@@ -1,1 +1,1 @@
-cd9018713bd4827be2e32e2531228955562863c95e3385b37fdb8063daa1e1fe  
download/bismark_v0.19.1.tar.gz
+2ceb620cfc3f1c869f4bda656ab01c242f1da7ec01615b0d23b28c702147a337  
download/0.23.1.tar.gz