From 8b6bd98a183be077709566e01319dcb556841618 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Mon, 15 Jan 2024 12:48:26 +0100 Subject: [PATCH] cleanup for #220 --- 220_SOAPdenovo-Trans/Error_log.txt | 69 ------------------- .../SOAPdenovo-Trans-1.0.4-intel-2023a.eb | 36 ---------- .../SOAPdenovo-Trans-1.0.5-GCC-12.3.0.eb | 35 ---------- ...SOAPdenovo-Trans-1.0.5-fix-makefiles.patch | 30 -------- .../SOAPdenovo-Trans-1.0.5-intel-2023a.eb | 35 ---------- 220_SOAPdenovo-Trans/zlib-1.3-intel-2023a.eb | 23 ------- 6 files changed, 228 deletions(-) delete mode 100644 220_SOAPdenovo-Trans/Error_log.txt delete mode 100644 220_SOAPdenovo-Trans/SOAPdenovo-Trans-1.0.4-intel-2023a.eb delete mode 100644 220_SOAPdenovo-Trans/SOAPdenovo-Trans-1.0.5-GCC-12.3.0.eb delete mode 100644 220_SOAPdenovo-Trans/SOAPdenovo-Trans-1.0.5-fix-makefiles.patch delete mode 100644 220_SOAPdenovo-Trans/SOAPdenovo-Trans-1.0.5-intel-2023a.eb delete mode 100644 220_SOAPdenovo-Trans/zlib-1.3-intel-2023a.eb diff --git a/220_SOAPdenovo-Trans/Error_log.txt b/220_SOAPdenovo-Trans/Error_log.txt deleted file mode 100644 index 9c1769f2..00000000 --- a/220_SOAPdenovo-Trans/Error_log.txt +++ /dev/null @@ -1,69 +0,0 @@ -Change to GCC toolchain from intel works - -tried 1.0.4 insted of 1.0.5. -> same error - -ERROR: -== 2024-01-09 14:29:43,720 run.py:246 INFO running cmd: make -j 8 && make 127mer=1 -== 2024-01-09 14:29:50,352 build_log.py:171 ERROR EasyBuild crashed with an error (at easybuild/easybuild-framework/easybuild/base/exceptions.py:126 in __init__): cmd " make --j 8 && make 127mer=1" exited with exit code 2 and output: -Compiling arc.c... ^MCompiling attachPEinfo.c... ^MCompiling bubble.c... ^MCompiling check. -c... ^MCompiling concatenateEdge.c... ^MCompiling compactEdge.c... ^MCompiling connect.c... - ^M../SOAPdenovo-Trans-31mer cleaning done. -Compiling contig.c... ^Mcontig.c:220:2: error: call to undeclared function 'output_pool'; ISO C99 and later do not support implicit function declar -ations [-Wimplicit-function-declaration] - output_pool(fileName); - ^ -contig.c:248:2: error: call to undeclared function 'deleteWeakEdge'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration] - deleteWeakEdge(de); - ^ -contig.c:253:2: error: call to undeclared function 'deleteUnlikeArc'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration] - deleteUnlikeArc(); - ^ -contig.c:270:2: error: call to undeclared function 'deleteShortContig'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration] - deleteShortContig(cut_length); - ^ -4 errors generated. -Error in command: icx -c -fomit-frame-pointer -O2 -xHost -ftz -fp-speculation=safe -fp-model precise -DMER31 -m64 -Iinc contig.c -Compiling cutTipPreGraph.c... ^MCompiling darray.c... ^MCompiling cutTip_graph.c... ^MCompi -ling dfib.c... ^MCompiling dfibHeap.c... ^MCompiling fib.c... ^MCompiling fibHeap.c... - ^Mfib.c:142:13: warning: implicit truncation from 'int' to a one-bit wide bit-field changes value from 1 to -1 [-Wsingle-bit-bitfield-constant-conversi -on] - n->fh_keys = 1; - ^ ~ -cutTipPreGraph.c:137:53: warning: format specifies type 'unsigned long long' but the argument has type 'kmer_t *' (aka 'struct kmer_st *') [-Wformat] - printf ("kmer %llx not found, node1 %llx\n", word,node1); - ~~~~ ^~~~~ -cutTipPreGraph.c:202:55: warning: format specifies type 'unsigned long long' but the argument has type 'kmer_t *' (aka 'struct kmer_st *') [-Wformat] - printf ("kmer %llx not found, node1 %llx\n", word,node1); - ~~~~ ^~~~~ -cutTipPreGraph.c:254:55: warning: format specifies type 'unsigned long long' but the argument has type 'kmer_t *' (aka 'struct kmer_st *') [-Wformat] - printf ("kmer %llx not found, node1 %llx\n", word,node1); - ~~~~ ^~~~~ -cutTipPreGraph.c:1010:1: warning: non-void function does not return a value in all control paths [-Wreturn-type] -} -^ -Compiling hashFunction.c... ^MCompiling kmer.c... ^MCompiling lib.c... ^MCompiling loadGrap -h.c... ^M1 warning generated. -Compiling loadPath.c... ^MCompiling loadPreGraph.c... ^M4 warnings generated. -2 warnings and 4 errors generated. -Error in command: icx -c -fomit-frame-pointer -O2 -xHost -ftz -fp-speculation=safe -fp-model precise -DMER31 -m64 -Iinc scaffold.c -icx -fomit-frame-pointer -O2 -xHost -ftz -fp-speculation=safe -fp-model precise -DMER31 -m64 -L/apps/gent/RHEL8/cascadelake-ib/software/zlib/1.2.13-GCCcore-12.3.0/lib64 -L/app -s/gent/RHEL8/cascadelake-ib/software/zlib/1.2.13-GCCcore-12.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/imkl/2023.1.0/mkl/2023.1.0/lib/intel64 -L/apps/gent/RHEL8/cascad -elake-ib/software/intel-compilers/2023.1.0/compiler/2023.1.0/linux/compiler/lib/intel64 -o ../SOAPdenovo-Trans-31mer arc.o attachPEinfo.o bubble.o check.o compactEdge.o concat -enateEdge.o connect.o contig.o cutTipPreGraph.o cutTip_graph.o darray.o dfib.o dfibHeap.o fib.o fibHeap.o hashFunction.o kmer.o lib.o loadGraph.o loadPath.o loadPreGraph.o loc -alAsm.o main.o map.o mem_manager.o newhash.o node2edge.o orderContig.o output_contig.o output_pregraph.o output_scaffold.o pregraph.o prlHashCtg.o prlHashReads.o prlRead2Ctg.o - prlRead2path.o prlReadFillGap.o read2scaf.o readInterval.o stack.o readseq1by1.o ReadTrace.o scaffold.o searchPath.o seq.o splitReps.o -liomp5 -lpthread -lrt -lbam -lz -L./ -inc -... -icx: error: no such file or directory: 'contig.o' -icx: error: no such file or directory: 'output_pregraph.o' -icx: error: no such file or directory: 'scaffold.o' -make: *** [Makefile:76: SOAPdenovo] Error 1 - (at easybuild/easybuild-framework/easybuild/tools/run.py:681 in parse_cmd_output) -== 2024-01-09 14:29:50,352 build_log.py:267 INFO ... (took 6 secs) -== 2024-01-09 14:29:50,352 filetools.py:2012 INFO Removing lock /user/gent/470/vsc47063/.local/easybuild/software/.locks/_user_gent_470_vsc47063_.local_easybuild_software_SOAP -denovo-Trans_1.0.5-intel-2023a.lock... -== 2024-01-09 14:29:50,354 filetools.py:383 INFO Path /user/gent/470/vsc47063/.local/easybuild/software/.locks/_user_gent_470_vsc47063_.local_easybuild_software_SOAPdenovo-Tra -ns_1.0.5-intel-2023a.lock successfully removed. -== 2024-01-09 14:29:50,354 filetools.py:2016 INFO Lock removed: /user/gent/470/vsc47063/.local/easybuild/software/.locks/_user_gent_470_vsc47063_.local_easybuild_software_SOAP -denovo-Trans_1.0.5-intel-2023a.lock \ No newline at end of file diff --git a/220_SOAPdenovo-Trans/SOAPdenovo-Trans-1.0.4-intel-2023a.eb b/220_SOAPdenovo-Trans/SOAPdenovo-Trans-1.0.4-intel-2023a.eb deleted file mode 100644 index 8301a794..00000000 --- a/220_SOAPdenovo-Trans/SOAPdenovo-Trans-1.0.4-intel-2023a.eb +++ /dev/null @@ -1,36 +0,0 @@ -easyblock = 'MakeCp' - -name = 'SOAPdenovo-Trans' -version = '1.0.4' - -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': 'intel', 'version': '2023a'} - -source_urls = ['https://github.com/aquaskyline/SOAPdenovo-Trans/archive/'] -sources = ['%(version)s.tar.gz'] -checksums = [ - '378a54cde0ebe240fb515ba67197c053cf95393645c1ae1399b3a611be2a9795', # 1.0.4.tar.gz - '15c420a5e2c2a5a5837dbb1223a6b02b78f059b162e82952c7ceee83fdfdcffb', # SOAPdenovo-Trans-1.0.4-fix-makefiles.patch -] - -patches = ['%(name)s-1.0.4-fix-makefiles.patch'] - -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/220_SOAPdenovo-Trans/SOAPdenovo-Trans-1.0.5-GCC-12.3.0.eb b/220_SOAPdenovo-Trans/SOAPdenovo-Trans-1.0.5-GCC-12.3.0.eb deleted file mode 100644 index 90179657..00000000 --- a/220_SOAPdenovo-Trans/SOAPdenovo-Trans-1.0.5-GCC-12.3.0.eb +++ /dev/null @@ -1,35 +0,0 @@ -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/220_SOAPdenovo-Trans/SOAPdenovo-Trans-1.0.5-fix-makefiles.patch b/220_SOAPdenovo-Trans/SOAPdenovo-Trans-1.0.5-fix-makefiles.patch deleted file mode 100644 index edb305d0..00000000 --- a/220_SOAPdenovo-Trans/SOAPdenovo-Trans-1.0.5-fix-makefiles.patch +++ /dev/null @@ -1,30 +0,0 @@ -# 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"; - diff --git a/220_SOAPdenovo-Trans/SOAPdenovo-Trans-1.0.5-intel-2023a.eb b/220_SOAPdenovo-Trans/SOAPdenovo-Trans-1.0.5-intel-2023a.eb deleted file mode 100644 index d5dbda49..00000000 --- a/220_SOAPdenovo-Trans/SOAPdenovo-Trans-1.0.5-intel-2023a.eb +++ /dev/null @@ -1,35 +0,0 @@ -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': 'intel', 'version': '2023a'} - -source_urls = ['https://github.com/aquaskyline/SOAPdenovo-Trans/archive/'] -sources = ['%(version)s.tar.gz'] -patches = ['%(name)s-1.0.4-fix-makefiles.patch'] -checksums = [ - {'1.0.5.tar.gz': 'c1903c0d81142270db95916e2833400f72c4841b5c9194f182c19ebda418936f'}, - {'SOAPdenovo-Trans-1.0.4-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/220_SOAPdenovo-Trans/zlib-1.3-intel-2023a.eb b/220_SOAPdenovo-Trans/zlib-1.3-intel-2023a.eb deleted file mode 100644 index b3c10600..00000000 --- a/220_SOAPdenovo-Trans/zlib-1.3-intel-2023a.eb +++ /dev/null @@ -1,23 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'zlib' -version = '1.3' - -homepage = 'http://www.zlib.net/' -description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, - not covered by any patents -- lossless data-compression library for use on virtually any - computer hardware and operating system.""" - -toolchain = {'name': 'intel', 'version': '2023a'} -toolchainopts = {'pic': True} - -source_urls = ['http://www.zlib.net/'] -sources = ['zlib-%(version)s.tar.gz'] -checksums = ['ff0ba4c292013dbc27530b3a81e1f9a813cd39de01ca5e0f8bf355702efa593e'] - -sanity_check_paths = { - 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'lib'