diff --git a/easybuild/easyconfigs/s/SOAPdenovo-Trans/SOAPdenovo-Trans-1.0.5-GCC-12.3.0.eb b/easybuild/easyconfigs/s/SOAPdenovo-Trans/SOAPdenovo-Trans-1.0.5-GCC-12.3.0.eb new file mode 100644 index 00000000000..901796573cc --- /dev/null +++ b/easybuild/easyconfigs/s/SOAPdenovo-Trans/SOAPdenovo-Trans-1.0.5-GCC-12.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'MakeCp' + +name = 'SOAPdenovo-Trans' +version = '1.0.5' + +homepage = 'http://soap.genomics.org.cn/SOAPdenovo-Trans.html' +description = """SOAPdenovo-Trans is a de novo transcriptome assembler basing on the SOAPdenovo framework, +adapt to alternative splicing and different expression level among transcripts. +""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/aquaskyline/SOAPdenovo-Trans/archive/'] +sources = ['%(version)s.tar.gz'] +patches = ['%(name)s-1.0.5-fix-makefiles.patch'] +checksums = [ + {'1.0.5.tar.gz': 'c1903c0d81142270db95916e2833400f72c4841b5c9194f182c19ebda418936f'}, + {'SOAPdenovo-Trans-1.0.5-fix-makefiles.patch': '15c420a5e2c2a5a5837dbb1223a6b02b78f059b162e82952c7ceee83fdfdcffb'}, +] + +dependencies = [('zlib', '1.2.13')] + +start_dir = 'src' + +buildopts = ' && make 127mer=1' + +files_to_copy = [(['../SOAPdenovo-Trans-127mer', '../SOAPdenovo-Trans-31mer'], 'bin'), '../LICENSE', + '../README.md', '../VERSION'] + +sanity_check_paths = { + 'files': ['bin/SOAPdenovo-Trans-127mer', 'bin/SOAPdenovo-Trans-31mer'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SOAPdenovo-Trans/SOAPdenovo-Trans-1.0.5-fix-makefiles.patch b/easybuild/easyconfigs/s/SOAPdenovo-Trans/SOAPdenovo-Trans-1.0.5-fix-makefiles.patch new file mode 100644 index 00000000000..edb305d0083 --- /dev/null +++ b/easybuild/easyconfigs/s/SOAPdenovo-Trans/SOAPdenovo-Trans-1.0.5-fix-makefiles.patch @@ -0,0 +1,30 @@ +# Fix makefile to use EB values +# Ward Poelmans +--- SOAPdenovo-Trans-src-v1.04.orig/src/Makefile 2014-04-15 04:37:16.000000000 +0200 ++++ SOAPdenovo-Trans-src-v1.04/src/Makefile 2017-08-23 07:54:58.108664416 +0200 +@@ -1,5 +1,5 @@ +-CC= gcc +-CFLAGS= -O3 -fomit-frame-pointer -static ++CC := $(CC) ++CFLAGS := -fomit-frame-pointer $(CFLAGS) + #CFLAGS= -O3 -g -D_DEBUG + DFLAGS= + +@@ -32,7 +32,7 @@ + INCLUDES= -Iinc + SUBDIRS= . + LIBPATH= +-LIBS= -pthread -lm -lrt -lbam -lz -L./inc ++LIBS := $(LIBS) -lrt -lbam -lz -L./inc + EXTRA_FLAGS= + + BIT_ERR = 0 +@@ -73,7 +73,7 @@ + @test $(BIT_ERR) != 1 || sh -c 'echo "Fatal: 64bit CPU and Operating System required!";false;' + + SOAPdenovo: envTest $(OBJS) +- @$(CC) $(CFLAGS) -o $(PROG) $(OBJS) $(LIBPATH) $(LIBS) $(ENTRAFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $(PROG) $(OBJS) $(LIBPATH) $(LIBS) $(ENTRAFLAGS) + @printf "Linking...\r" + @printf "$(PROG) compilation done.\n"; +