#271 working ABySS

271_phyluce/ABySS-2.3.7-foss-2023a.eb

@@ -7,24 +7,31 @@ homepage = 'https://www.bcgsc.ca/platform/bioinfo/software/abyss'
 description = """Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler"""
 
 toolchain = {'name': 'foss', 'version': '2023a'}
-# toolchainopts = {'usempi': True, 'cstd': 'c++11'}
+toolchainopts = {'usempi': True, 'cstd': 'c++17'}
+# toolchainopts = {'usempi': True}
 
 source_urls = ['http://github.com/bcgsc/abyss/releases/download/%(version)s/']
 sources = [SOURCELOWER_TAR_GZ]
 checksums = ['ba37780e79ec3aa359b6003e383caef13479a87f4d0022af01b86398f9ffca1f']
 
 dependencies = [
+    ('Autoconf', '2.71'),
+    ('Automake', '1.16.5'),
     ('Boost', '1.82.0'),
     ('sparsehash', '2.0.4'),
-    ('SQLite', '3.42.0'),
+    ('OpenMPI', '4.1.5'),
+    # ('SQLite', '3.42.0'),
     ('btllib', '1.7.0'),
 ]
 
-configopts = 'CXXFLAGS="$CXXFLAGS -Wno-error=deprecated-copy"'
+preconfigopts = "./autogen.sh && "
+configopts = 'CXXFLAGS="$CXXFLAGS -Wno-error"'
 
 sanity_check_paths = {
     'files': ["bin/ABYSS", "bin/ABYSS-P"],
     'dirs': []
 }
 
+sanity_check_commands = ['ABYSS --help']
+
 moduleclass = 'bio'

271_phyluce/error_log.txt

@@ -0,0 +1,36 @@
+Error during run Abyss:
+ERROR_1:
+mpicxx -std=c++11 -DHAVE_CONFIG_H -I. -I..   -I/tmp/vsc47063/easybuild/build/ABySS/2.3.7/foss-2023a/abyss-2.3.7      -I/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-amper-12.3.0/include -I/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/OpenMPI/4.1.5-GCC-12.3.0/include -I/scratch/gent/vo/001/gelake-ampere-ib/software/sparsehash/2.0.4-GCCcore-12.3.0/include -I/apps/gent/RHEL8/cascadelake-ib/software/Boost/1.82.0-GCC-12.3.0/include -I/scratch/gRHEL8/cascadelake-ampere-ib/software/FFTW.MPI/3.3.10-gompi-2023a/include -I/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.3.1-GCC-12.3.0/include -ib/software/FlexiBLAS/3.3.1-GCC-12.3.0/include/flexiblas -isystem/tmp/vsc47063/easybuild/build/ABySS/2.3.7/foss-2023a/abyss-2.3.7/boost_1_56_0 -Wall -Wedeclarations -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -O2 -ftree-vectorize -march=native -fno-math-errno -Wno-error=deprect_a-RUtils.Tpo .deps/libralgorithmsshort_a-RUtils.Po
+mv -f .deps/libralgorithmsshort_a-RUtils.Tpo .deps/libralgorithmsshort_a-RUtils.Po
+In file included from /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/btllib/1.7.0-GCC-12.3.0/include/btllib/nthash.hpp:12,
+                 from /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/btllib/1.7.0-GCC-12.3.0/include/btllib/bloom_filter.hpp:4,
+                 from BloomFilters.h:4,
+                 from RAlgorithmsShort.h:4,
+                 from RResolverShort.cpp:7:
+/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/btllib/1.7.0-GCC-12.3.0/include/btllib/hashing_internals.hpp:554:11: error:
+ilable with -std=c++17 or -std=gnu++17 [-Werror=c++17-extensions]
+  554 | constexpr inline uint64_t AA_SEED_A = 0xf56d6192468323df;
+      |           ^~~~~~
+/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/btllib/1.7.0-GCC-12.3.0/include/btllib/hashing_internals.hpp:555:11: error:
+ilable with -std=c++17 or -std=gnu++17 [-Werror=c++17-extensions]
+  555 | constexpr inline uint64_t AA_SEED_C = 0x9b0b2fd724e1e1d2;
+      |           ^~~~~~
+/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/btllib/1.7.0-GCC-12.3.0/include/btllib/hashing_internals.hpp:556:11: error:
+ilable with -std=c++17 or -std=gnu++17 [-Werror=c++17-extensions]
+  556 | constexpr inline uint64_t AA_SEED_D = 0xe8c583296b03c7af;
+.....
+mv -f .deps/libralgorithmsshort_a-SequenceTree.Tpo .deps/libralgorithmsshort_a-SequenceTree.Po
+cc1plus: all warnings being treated as errors
+make[2]: *** [Makefile:555: abyss_rresolver_short-RResolverShort.o] Error 1
+make[2]: *** Waiting for unfinished jobs....
+cc1plus: all warnings being treated as errors
+make[2]: *** [Makefile:499: libralgorithmsshort_a-BloomFilters.o] Error 1
+mv -f .deps/abyss_rresolver_short-Contigs.Tpo .deps/abyss_rresolver_short-Contigs.Po
+mv -f .deps/libralgorithmsshort_a-Contigs.Tpo .deps/libralgorithmsshort_a-Contigs.Po
+cc1plus: all warnings being treated as errors
+make[2]: *** [Makefile:485: libralgorithmsshort_a-RAlgorithmsShort.o] Error 1
+make[2]: Leaving directory '/tmp/vsc47063/easybuild/build/ABySS/2.3.7/foss-2023a/abyss-2.3.7/RResolver'
+make[1]: *** [Makefile:488: all-recursive] Error 1
+make[1]: Leaving directory '/tmp/vsc47063/easybuild/build/ABySS/2.3.7/foss-2023a/abyss-2.3.7'
+make: *** [Makefile:408: all] Error 2
+ (at easybuild/easybuild-framework/easybuild/tools/run.py:682 in parse_cmd_output)