Merge pull request #19530 from pavelToman/20240109153711_new_pr_SOAPd…

…enovo-Trans105

{bio}[GCC/12.3.0] SOAPdenovo-Trans v1.0.5

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'

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 <[email protected]>
+--- 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";
+