[Gsrc-commit] trunk r9720: update megahit to master

[Carl Hansen]

------------------------------------------------------------
revno: 9720
revision-id: carlhansen@gnu.org-20231128012302-j4euond2om7lw21b
parent: carlhansen@gnu.org-20231127224253-7c8ydizkcpxuttui
committer: carlhansen@gnu.org
branch nick: trunk
timestamp: Mon 2023-11-27 17:23:02 -0800
message:
  update megahit to master
added:
  pkg/bio/megahit/               megahit-20231128012226-sy01vauba1pvymee-1
  pkg/bio/megahit/Makefile       makefile-20231128012226-sy01vauba1pvymee-3
  pkg/bio/megahit/config.mk      config.mk-20231128012226-sy01vauba1pvymee-2

=== added directory 'pkg/bio/megahit'
=== added file 'pkg/bio/megahit/Makefile'
--- a/pkg/bio/megahit/Makefile  1970-01-01 00:00:00 +0000
+++ b/pkg/bio/megahit/Makefile  2023-11-28 01:23:02 +0000
@@ -0,0 +1,72 @@
+# Copyright ©2023 Carl Hansen <carlhansen@gnu.org>
+#
+# This file is part of GSRC, the GNU Source Release Collection.
+# http://www.gnu.org/software/gsrc
+#
+# GSRC is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# GSRC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public
+# License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GSRC.  If not, see <http://www.gnu.org/licenses/>.
+
+# Send bug reports and comments about GSRC problems to bug-gsrc@gnu.org
+
+NAME = MEGAHIT
+GARNAME = megahit
+GARVERSION = master
+HOME_URL = http://github.com/voutcn/megahit
+DESCRIPTION = NGS assembler for genomes
+define BLURB
+MEGAHIT is an ultra-fast and memory-efficient NGS assembler. It is
+optimized for metagenomes, but also works well on generic single genome
+assembly (small or mammalian size) and single-cell assembly.
+endef
+LICENSE = GPLv3
+CITE =
+
+######################################################################
+# https://github.com/voutcn/megahit
+MASTER_SITES = $(MASTER_GITHUB)
+MASTER_SUBDIR = voutcn
+GIT_PATH = $(MASTER_SITES)$(MASTER_SUBDIR)/$(GARNAME).git
+
+SIGFILES =
+
+GIT_REVISION = master
+#GITSRC =  $(BASEDIRABS)/$(DOWNLOADDIRGIT)/$(GARNAME)
+WORKSRC =               $(DOWNLOADDIRGIT)/$(GARNAME)
+WORKOBJ =  $(WORKDIR)/$(DISTNAME)-build
+
+BUILDDEPS = 
+LIBDEPS =
+
+CONFIGURE_SCRIPTS =
+BUILD_SCRIPTS =  my
+#INSTALL_SCRIPTS = my
+######################################################################
+
+include ../../../gar/gar.lib/cmake.mk
+include config.mk
+
+# work in progress
+
+pre-build: fetch-gitrecursive
+       cd $(WORKSRC) && git submodule update --init
+       mkdir -p $(WORKOBJ)
+       cmake -B $(WORKOBJ) -S $(WORKSRC) -DCMAKE_BUILD_TYPE=Release 
+
+#todo  pathc include <stdint> after fetch before build...
+build-my:  pre-build
+       $(MAKE) -C $(WORKOBJ)   
+       $(MAKE) -C $(WORKOBJ) simple_test       
+
+install-my:
+       $(INSTALL_BIN) $(WORKSRC)/
+

=== added file 'pkg/bio/megahit/config.mk'
--- a/pkg/bio/megahit/config.mk 1970-01-01 00:00:00 +0000
+++ b/pkg/bio/megahit/config.mk 2023-11-28 01:23:02 +0000
@@ -0,0 +1,4 @@
+## Configuration options
+
+CONFIGURE_OPTS ?= 
+BUILD_OPTS ?=