{bio}[foss/2018b] bmtagger v3.101, SRPRISM v3.0.0

easybuild/easyconfigs/b/bmtagger/bmtagger-3.101-foss-2018b.eb

@@ -0,0 +1,37 @@
+easyblock = 'MakeCp'
+
+name = 'bmtagger'
+version = '3.101'
+
+homepage = 'ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/bmtagger/'
+description = "Best Match Tagger for removing human reads from metagenomics datasets"
+
+toolchain = {'name': 'foss', 'version': '2018b'}
+toolchainopts = {'cstd': 'c++98'}
+
+source_urls = ['ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/bmtagger/']
+sources = [{'download_filename': 'bmtools.tar.gz', 'filename': 'bmtools-%(version)s.tar.gz'}]
+patches = ['bmtagger-%(version)s_fix-hardcoding.patch']
+checksums = [
+    '81ac6d47aa478c2e0ef760f15b9c71e1c52430c96a2c8d064667ebbef148e873',  # bmtools-3.101.tar.gz
+    '8779edd4dab6c0a3bc1bbcc5f265d61ccfd685972a0570bc3a84f5a131972195',  # bmtagger-3.101_fix-hardcoding.patch
+]
+
+dependencies = [
+    ('BLAST+', '2.7.1'),
+    ('SRPRISM', '3.0.0'),
+]
+
+files_to_copy = [(['bmtagger/bmfilter', 'bmtagger/bmtagger.sh', 'bmtagger/bmtool', 'bmtagger/extract_fullseq'], 'bin')]
+
+sanity_check_paths = {
+    'files': ['bin/bmfilter', 'bin/bmtagger.sh', 'bin/bmtool', 'bin/extract_fullseq'],
+    'dirs': [],
+}
+
+sanity_check_commands = [
+    "bmtool -h",
+    "bmfilter -h",
+]
+
+moduleclass = 'bio'

easybuild/easyconfigs/b/bmtagger/bmtagger-3.101_fix-hardcoding.patch

@@ -0,0 +1,11 @@
+fix hardcoding of compiler command & flags, by passing down $CXX, $CXX and $CXXFLAGS
+--- Makefile.orig	2014-02-21 01:20:50.000000000 +0100
++++ Makefile	2019-03-14 16:20:18.415277482 +0100
+@@ -4,6 +4,6 @@
+
+
+ all depend test clean:
+-	set -e ; for file in $(SUBDIRS) ; do make -C $$file $(MAKEFLAGS:%=-%) $@ ; done
++	set -e ; for file in $(SUBDIRS) ; do make -C $$file $@ CC="${CC}" CXX="${CXX}" FLAGS="${CFLAGS}"; done
+
+

easybuild/easyconfigs/s/SRPRISM/SRPRISM-3.0.0-foss-2018b.eb

@@ -0,0 +1,36 @@
+easyblock = 'MakeCp'
+
+name = 'SRPRISM'
+version = '3.0.0'
+
+homepage = 'https://github.com/ncbi/SRPRISM'
+description = "Single Read Paired Read Indel Substitution Minimizer"
+
+toolchain = {'name': 'foss', 'version': '2018b'}
+
+source_urls = ['https://github.com/ncbi/SRPRISM/archive/']
+sources = ['v%(version)s.tar.gz']
+patches = ['SRPRISM-%(version)s_fix-GCC-7.patch']
+checksums = [
+    'ff40ad5b3d41fa5980550425b5f7ad570f1ee830c158bfd6cb468372091e11f0',  # v3.0.0.tar.gz
+    'b65a594851f25e22fce28ad16732f110eec118a6f7125ecd7ea163f95b1f5121',  # SRPRISM-3.0.0_fix-GCC-7.patch
+]
+
+dependencies = [
+    ('NGS', '2.9.3', '-Java-1.8'),
+    ('bzip2', '1.0.6'),
+]
+
+prebuildopts = "cd srprism/lib && "
+buildopts = " && cd ../app && make"
+
+files_to_copy = [(['srprism/app/srprism'], 'bin')]
+
+sanity_check_paths = {
+    'files': ['bin/srprism'],
+    'dirs': [],
+}
+
+sanity_check_commands = ["srprism help"]
+
+moduleclass = 'bio'

easybuild/easyconfigs/s/SRPRISM/SRPRISM-3.0.0_fix-GCC-7.patch

@@ -0,0 +1,54 @@
+fix compilation with GCC 7.x
+author: Kenneth Hoste (HPC-UGent)
+see also https://github.com/ncbi/SRPRISM/issues/1
+--- srprism/lib/srprism/query_acct.hpp.orig	2019-03-14 17:53:26.960989751 +0100
++++ srprism/lib/srprism/query_acct.hpp	2019-03-14 18:47:10.461173398 +0100
+@@ -112,10 +112,10 @@
+
+         template< bool paired >
+         bool BestLevelFull( TQNum qn ) const
+-        { return query_info_[qn].BestLevelFull< paired >( res_lim_ ); }
++        { return query_info_[qn].template BestLevelFull< paired >( res_lim_ ); }
+
+         template< bool paired > int MaxErr( TQNum qn ) const
+-        { return query_info_[qn].MaxErr< paired >(); }
++        { return query_info_[qn].template MaxErr< paired >(); }
+
+         int GroupMaxErr( TQNum dup_idx ) const
+         { return t_scoring::template MaxErr< true >( dup_data_[dup_idx] ); }
+--- srprism/lib/srprism/query_store.hpp.orig	2019-03-14 17:58:03.219288045 +0100
++++ srprism/lib/srprism/query_store.hpp	2019-03-14 18:48:45.310588004 +0100
+@@ -662,7 +662,7 @@
+                     else AdjustMinRankInfo< t_scoring >( qn );
+                 }
+
+-                int max_err( qa->MaxErr< true >( qn ) );
++                int max_err( qa->template MaxErr< true >( qn ) );
+
+                 if( max_err < min_err ||
+                         (max_err == min_err && 
+@@ -687,7 +687,7 @@
+                         qn, align_len, n_err, n_gap, n_del, n_gopen ) );
+
+             if( res ) {
+-                int max_err( qa->MaxErr< false >( qn ) );
++                int max_err( qa->template MaxErr< false >( qn ) );
+
+                 if( max_err < min_err ||
+                         (max_err == min_err && 
+@@ -715,13 +715,13 @@
+         TSeqSize MaxQueryLen( void ) const { return max_query_len_; }
+
+         template< typename t_scoring, bool paired > int MaxErr( TQNum qn ) const
+-        { return GetScoringData< t_scoring >()->MaxErr< paired >( qn ); }
++        { return GetScoringData< t_scoring >()->template MaxErr< paired >( qn ); }
+
+         template< typename t_scoring, bool paired > int 
+         GroupMaxErr( TQNum qn ) const
+         {
+             if( IsUnique( qn ) || DupDataStart( qn )[N_MIN_RANK] == 0 ) {
+-                return GetScoringData< t_scoring >()->MaxErr< paired >( qn );
++                return GetScoringData< t_scoring >()->template MaxErr< paired >( qn );
+             }
+             else {
+                 return GetScoringData< t_scoring >()->GroupMaxErr(