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{bio}[GCC/12.3.0] SOAPdenovo-Trans v1.0.5 #19530

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Jan 10, 2024
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{bio}[GCC/12.3.0] SOAPdenovo-Trans v1.0.5 #19530

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35 changes: 35 additions & 0 deletions easybuild/easyconfigs/s/SOAPdenovo-Trans/SOAPdenovo-Trans-1.0.5-GCC-12.3.0.eb
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Original file line number Diff line number Diff line change
@@ -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'
30 changes: 30 additions & 0 deletions easybuild/easyconfigs/s/SOAPdenovo-Trans/SOAPdenovo-Trans-1.0.5-fix-makefiles.patch
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Original file line number Diff line number Diff line change
@@ -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";

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