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Merge pull request #10390 from easybuilders/4.2.x
release EasyBuild v4.2.0
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| Original file line number | Diff line number | Diff line change |
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@@ -10,3 +10,4 @@ dist/ | |
| *.swp | ||
| *.ropeproject/ | ||
| eb-*.log | ||
| /MANIFEST | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,6 +1,4 @@ | ||
| recursive-include easybuild * | ||
| include CONTRIBUTING.md | ||
| include LICENSE | ||
| include README.rst | ||
| include RELEASE_NOTES | ||
| include setup.py |
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44 changes: 44 additions & 0 deletions
44
easybuild/easyconfigs/a/ABRA2/ABRA2-2.22-iccifort-2019.5.281.eb
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,44 @@ | ||
| easyblock = 'MakeCp' | ||
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| name = 'ABRA2' | ||
| version = '2.22' | ||
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| homepage = 'https://github.com/mozack/abra2' | ||
| description = "Assembly Based ReAligner" | ||
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| toolchain = {'name': 'iccifort', 'version': '2019.5.281'} | ||
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| source_urls = ['https://github.com/mozack/abra2/archive/'] | ||
| sources = ['v%(version)s.tar.gz'] | ||
| patches = ['ABRA2-%(version)s_fix-Makefile.patch'] | ||
| checksums = [ | ||
| '99cd1e83ed48095241402b0334af553ee75311213c16a7d0f3109a28771960e9', # v2.22.tar.gz | ||
| '05090efb306fc84d09f007a848ce0d0472f8633633b0a6eaf86ab075d092bc0d', # ABRA2-2.22_fix-Makefile.patch | ||
| ] | ||
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| builddependencies = [('Maven', '3.6.3', '', True)] | ||
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| dependencies = [ | ||
| ('Java', '11', '', True), | ||
| ('BWA', '0.7.17'), | ||
| ] | ||
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| parallel = 1 | ||
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| buildopts = 'CXX="$CXX" CXXFLAGS="$CXXFLAGS"' | ||
| buildopts += '&& make standalone CXX="$CXX" CXXFLAGS="$CXXFLAGS"' | ||
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| files_to_copy = [ | ||
| (['abra'], 'bin'), | ||
| (['target/libAbra.%s' % SHLIB_EXT], 'lib'), | ||
| 'target/abra2-%(version)s-jar-with-dependencies.jar', | ||
| ] | ||
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| postinstallcmds = ["cd %(installdir)s && mv abra2-%(version)s-jar-with-dependencies.jar abra2-%(version)s.jar"] | ||
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| sanity_check_paths = { | ||
| 'files': ['abra2-%(version)s.jar', 'bin/abra', 'lib/libAbra.%s' % SHLIB_EXT], | ||
| 'dirs': [], | ||
| } | ||
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| moduleclass = 'bio' |
32 changes: 32 additions & 0 deletions
32
easybuild/easyconfigs/a/ABRA2/ABRA2-2.22_fix-Makefile.patch
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,32 @@ | ||
| * don't hardcode g++ or "-g -O2" | ||
| * fix source filename for standalone build | ||
| author: Kenneth Hoste (HPC-UGent) | ||
| --- abra2-2.22/Makefile.orig 2020-03-28 11:40:49.094222081 +0100 | ||
| +++ abra2-2.22/Makefile 2020-03-28 11:41:38.732466934 +0100 | ||
| @@ -1,6 +1,9 @@ | ||
| # Make file for ABRA | ||
| # libAbra is invoked from the ABRA java code | ||
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| +CXX:=g++ | ||
| +CXXFLAGS:=-g -O2 | ||
| + | ||
| SRCDIR=src/main/c | ||
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| all: clean native java | ||
| @@ -12,13 +15,13 @@ | ||
| mkdir target | ||
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| native: mktargetdir | ||
| - g++ -g -O2 -I$(SRCDIR) -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux -shared -fPIC $(SRCDIR)/assembler.cpp $(SRCDIR)/sg_aligner.cpp -o target/libAbra.so | ||
| + $(CXX) $(CXXFLAGS) -I$(SRCDIR) -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux -shared -fPIC $(SRCDIR)/assembler.cpp $(SRCDIR)/sg_aligner.cpp -o target/libAbra.so | ||
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| standalone: | ||
| - g++ -g -I$(SRCDIR) -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux $(SRCDIR)/assembler.c -o abra | ||
| + $(CXX) $(CXXFLAGS) -I$(SRCDIR) -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux $(SRCDIR)/assembler.cpp -o abra | ||
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| sga: | ||
| - g++ -g -O2 -I$(SRCDIR) -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux $(SRCDIR)/sg_aligner.cpp -o sga | ||
| + $(CXX) $(CXXFLAGS) -I$(SRCDIR) -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux $(SRCDIR)/sg_aligner.cpp -o sga | ||
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| clean: | ||
| rm -rf target |
42 changes: 42 additions & 0 deletions
42
easybuild/easyconfigs/a/ABRicate/ABRicate-0.9.9-gompi-2019a-Perl-5.28.1.eb
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| @@ -0,0 +1,42 @@ | ||
| # Author: Pavel Grochal (INUITS) | ||
| # License: GPLv2 | ||
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| easyblock = 'Tarball' | ||
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| name = 'ABRicate' | ||
| version = '0.9.9' | ||
| versionsuffix = '-Perl-%(perlver)s' | ||
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| homepage = 'https://github.com/tseemann/abricate' | ||
| description = "Mass screening of contigs for antimicrobial and virulence genes" | ||
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| toolchain = {'name': 'gompi', 'version': '2019a'} | ||
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| # https://github.com/tseemann/abricate | ||
| github_account = 'tseemann' | ||
| source_urls = [GITHUB_LOWER_SOURCE] | ||
| sources = ['v%(version)s.zip'] | ||
| checksums = ['a2bf30f8cc53292b6c043a63975fb51c7043b59565edad5b16e5995cc006d3bc'] | ||
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| dependencies = [ | ||
| ('Perl', '5.28.1'), | ||
| ('any2fasta', '0.4.2', versionsuffix), | ||
| ('BioPerl', '1.7.2', versionsuffix), | ||
| ('BLAST+', '2.9.0'), | ||
| ] | ||
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| postinstallcmds = ['%(installdir)s/bin/abricate --setupdb'] | ||
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| sanity_check_paths = { | ||
| 'files': ['bin/abricate', 'bin/abricate-get_db'], | ||
| 'dirs': ['db'], | ||
| } | ||
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| sanity_check_commands = [ | ||
| "abricate --help", | ||
| "abricate --list", | ||
| ] | ||
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| modloadmsg = "abricate databases are located in $EBROOTABRICATE/db\n" | ||
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| moduleclass = 'bio' |
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