adding easyconfigs: DETONATE-1.11-GCC-12.3.0.eb, SAMtools-0.1.20-GCC-…

…12.3.0.eb, sparsehash-2.0.4-GCCcore-12.3.0.eb and patches: DETONATE-1.11_fix-deps.patch, DETONATE-1.11_include-fix.patch, DETONATE-1.11_Intel-fixes.patch, SAMtools-0.1.20_Makefile-ncurses.patch

easybuild/easyconfigs/d/DETONATE/DETONATE-1.11-GCC-12.3.0.eb

@@ -0,0 +1,60 @@
+easyblock = 'MakeCp'
+
+name = 'DETONATE'
+version = '1.11'
+
+homepage = 'http://deweylab.biostat.wisc.edu/detonate/'
+description = """DETONATE (DE novo TranscriptOme rNa-seq Assembly with or without the Truth Evaluation)
+ consists of two component packages, RSEM-EVAL and REF-EVAL. Both packages are mainly intended to be used
+ to evaluate de novo transcriptome assemblies, although REF-EVAL can be used to compare sets of any kinds
+ of genomic sequences."""
+
+toolchain = {'name': 'GCC', 'version': '12.3.0'}
+
+toolchainopts = {'cstd': 'c++11'}
+
+source_urls = ['http://deweylab.biostat.wisc.edu/detonate/']
+sources = ['detonate-1.11.tar.gz']
+patches = [
+    'DETONATE-%(version)s_fix-deps.patch',
+    'DETONATE-%(version)s_Intel-fixes.patch',
+    'DETONATE-%(version)s_include-fix.patch'
+]
+checksums = [
+    {'detonate-1.11.tar.gz': 'e1d04af1b1d2504942a6941b346d430157da6117fac043b7ee83274717d99714'},
+    {'DETONATE-1.11_fix-deps.patch': '0ab353f66d5459e1fa18fa214026589fe214365f3532a3b9ea182757c7547691'},
+    {'DETONATE-1.11_Intel-fixes.patch': 'c72a18250857883e7075ac512bbbd532e61a1aab38868d0dc932ca4bdc412817'},
+    {'DETONATE-1.11_include-fix.patch': '9071fc8dbc6bfc26a9c4bb60befca890a26acf9668df2815a7f0038d8bcdd9f6'},
+]
+
+builddependencies = [
+    ('CMake', '3.26.3'), 
+    ('SAMtools', '0.1.20'),
+    ]
+
+dependencies = [
+    ('Boost', '1.82.0'),
+    ('sparsehash', '2.0.4'),
+    ('BamTools','2.5.2'),
+    ('zlib', '1.2.13'),
+]
+
+start_dir = 'ref-eval'
+
+buildopts = 'CXX="$CXX" CXXFLAGS="$CXXFLAGS -fopenmp" && cd ../rsem-eval && make CC="$CXX" CFLAGS="$CXXFLAGS"'
+
+runtest = 'test'
+
+files_to_copy = [(['ref-eval', 'ref-eval-estimate-true-assembly', '../rsem-eval/rsem-*'], 'bin')]
+
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in ['ref-eval', 'ref-eval-estimate-true-assembly', 'rsem-build-read-index',
+                                     'rsem-eval-calculate-score', 'rsem-eval-estimate-transcript-length-distribution',
+                                     'rsem-eval-run-em', 'rsem-extract-reference-transcripts',
+                                     'rsem-parse-alignments', 'rsem-plot-model', 'rsem-preref', 'rsem-sam-validator',
+                                     'rsem-scan-for-paired-end-reads', 'rsem-simulate-reads',
+                                     'rsem-synthesis-reference-transcripts']],
+    'dirs': [],
+}
+
+moduleclass = 'bio'

easybuild/easyconfigs/d/DETONATE/DETONATE-1.11_Intel-fixes.patch

@@ -0,0 +1,48 @@
+fix compilation issues that occur with Intel compilers
+error: no suitable conversion function from "std::basic_istream<char, std::char_traits<char>>" to "bool" exists
+
+author: Kenneth Hoste (HPC-UGent), with a bit of help from Ward Poelmans
+--- detonate-1.11/rsem-eval/SingleHit.h.orig	2018-01-23 11:01:34.269328898 +0100
++++ detonate-1.11/rsem-eval/SingleHit.h	2018-01-23 11:01:55.859848244 +0100
+@@ -43,7 +43,7 @@
+
+ bool SingleHit::read(std::istream& in) {
+ 	conprb = 0.0;
+-	return (in>>sid>>pos);
++	return static_cast<bool>(in>>sid>>pos);
+ }
+
+ void SingleHit::write(std::ostream& out) {
+--- detonate-1.11/rsem-eval/PairedEndHit.h.orig	2018-01-23 11:07:46.838260187 +0100
++++ detonate-1.11/rsem-eval/PairedEndHit.h	2018-01-23 11:08:12.628872625 +0100
+@@ -26,7 +26,7 @@
+
+ bool PairedEndHit::read(std::istream& in) {
+ 	conprb = 0.0;
+-    return (in>>sid>>pos>>insertL);
++    return static_cast<bool>(in>>pos>>insertL);
+ }
+
+ void PairedEndHit::write(std::ostream& out) {
+--- detonate-1.11/rsem-eval/buildReadIndex.cpp.orig	2018-01-23 13:58:46.313840541 +0100
++++ detonate-1.11/rsem-eval/buildReadIndex.cpp	2018-01-23 13:59:51.375415745 +0100
+@@ -35,15 +35,15 @@
+ 		streampos pos = fin.tellg();
+ 		success = true;
+
+-		success = (getline(fin, line));
++		success = static_cast<bool>(getline(fin, line));
+ 		if (!success) continue;
+-		success = (getline(fin, line));
++		success = static_cast<bool>(getline(fin, line));
+ 		if (!success) continue;
+
+ 		if (hasQ) {
+-			success = (getline(fin, line));
++			success = static_cast<bool>(getline(fin, line));
+ 			if (!success) continue;
+-			success = (getline(fin, line));
++			success = static_cast<bool>(getline(fin, line));
+ 			if (!success) continue;
+ 		}
+

easybuild/easyconfigs/d/DETONATE/DETONATE-1.11_fix-deps.patch

@@ -0,0 +1,144 @@
+- fix compilation flags, use $CFLAGS passed by EasyBuild
+- use Boost, SAMtools, sparsehash provided as dependencies via EasyBuild
+author: Kenneth Hoste (HPC-UGent)
+--- detonate-1.11/rsem-eval/Makefile.orig	2016-06-22 23:34:39.000000000 +0200
++++ detonate-1.11/rsem-eval/Makefile	2018-01-23 14:47:47.714929147 +0100
+@@ -7,18 +7,15 @@
+
+ all : $(PROGRAMS)
+
+-sam/libbam.a :
+-	cd sam ; ${MAKE} all
+-
+ Transcript.h : utils.h
+
+ Transcripts.h : utils.h my_assert.h Transcript.h
+
+ rsem-extract-reference-transcripts : utils.h my_assert.h GTFItem.h Transcript.h Transcripts.h extractRef.cpp
+-	$(CC) -Wall -O3 extractRef.cpp -o rsem-extract-reference-transcripts
++	$(CC) $(CFLAGS) extractRef.cpp -o rsem-extract-reference-transcripts
+
+ rsem-synthesis-reference-transcripts : utils.h my_assert.h Transcript.h Transcripts.h synthesisRef.cpp
+-	$(CC) -Wall -O3 synthesisRef.cpp -o rsem-synthesis-reference-transcripts
++	$(CC) $(CFLAGS) synthesisRef.cpp -o rsem-synthesis-reference-transcripts
+
+ BowtieRefSeqPolicy.h : RefSeqPolicy.h
+
+@@ -28,10 +25,10 @@
+
+
+ rsem-preref : preRef.o
+-	$(CC) preRef.o -o rsem-preref
++	$(CC) $(CFLAGS) preRef.o -o rsem-preref
+
+ preRef.o : utils.h RefSeq.h Refs.h PolyARules.h RefSeqPolicy.h AlignerRefSeqPolicy.h preRef.cpp
+-	$(CC) $(COFLAGS) preRef.cpp
++	$(CC) -c -I $(CFLAGS) preRef.cpp
+
+
+ SingleRead.h : Read.h
+@@ -49,14 +46,14 @@
+
+ SamParser.h : sam/sam.h sam/bam.h utils.h my_assert.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h Transcripts.h
+
+-rsem-parse-alignments : parseIt.o sam/libbam.a
+-	$(CC) -o rsem-parse-alignments parseIt.o sam/libbam.a -lz -lpthread 
++rsem-parse-alignments : parseIt.o
++	$(CC) -o rsem-parse-alignments parseIt.o ${EBROOTSAMTOOLS}/lib/libbam.a -lz -lpthread 
+
+ parseIt.o : utils.h RefSeq.h Refs.h GroupInfo.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h HitContainer.h SamParser.h Transcripts.h sam/sam.h sam/bam.h parseIt.cpp
+-	$(CC) -Wall -O2 -c -I. parseIt.cpp
++	$(CC) $(CFLAGS) -c -I. parseIt.cpp
+
+ rsem-build-read-index : utils.h buildReadIndex.cpp
+-	$(CC) -O3 buildReadIndex.cpp -o rsem-build-read-index
++	$(CC) $(CFLAGS) buildReadIndex.cpp -o rsem-build-read-index
+
+
+ simul.h : boost/random.hpp
+@@ -85,23 +82,23 @@
+
+ CalcEvalScore.h : utils.h my_assert.h Refs.h GroupInfo.h Transcript.h Transcripts.h ContigLengthDist.h
+
+-rsem-eval-run-em : EM.o sam/libbam.a
+-	$(CC) -o rsem-eval-run-em EM.o sam/libbam.a -lz -lpthread
++rsem-eval-run-em : EM.o
++	$(CC) -o rsem-eval-run-em EM.o ${EBROOTSAMTOOLS}/lib/libbam.a -lz -lpthread
+
+ EM.o : utils.h my_assert.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h Refs.h GroupInfo.h HitContainer.h ReadIndex.h ReadReader.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h ModelParams.h RefSeq.h RefSeqPolicy.h PolyARules.h Profile.h NoiseProfile.h Transcript.h Transcripts.h HitWrapper.h BamWriter.h sam/bam.h sam/sam.h simul.h sam_rsem_aux.h sampling.h boost/random.hpp WriteResults.h boost/math/distributions/negative_binomial.hpp ContigLengthDist.h CalcEvalScore.h EM.cpp 
+-	$(CC) $(COFLAGS) EM.cpp
++	$(CC) -c -I $(CFLAGS) EM.cpp
+
+ rsem-simulate-reads : simulation.o
+ 	$(CC) -o rsem-simulate-reads simulation.o
+
+ simulation.o : utils.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h Refs.h RefSeq.h GroupInfo.h Transcript.h Transcripts.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h Profile.h NoiseProfile.h simul.h boost/random.hpp WriteResults.h simulation.cpp
+-	$(CC) $(COFLAGS) simulation.cpp
++	$(CC) -c -I $(CFLAGS) simulation.cpp
+
+-rsem-sam-validator : sam/bam.h sam/sam.h my_assert.h samValidator.cpp sam/libbam.a
+-	$(CC) -O3 -Wall samValidator.cpp sam/libbam.a -lz -lpthread -o $@
++rsem-sam-validator : sam/bam.h sam/sam.h my_assert.h samValidator.cpp
++	$(CC) $(CFLAGS) samValidator.cpp ${EBROOTSAMTOOLS}/lib/libbam.a -lz -lpthread -o $@
+
+-rsem-scan-for-paired-end-reads : sam/bam.h sam/sam.h my_assert.h scanForPairedEndReads.cpp sam/libbam.a
+-	$(CC) -O3 -Wall scanForPairedEndReads.cpp sam/libbam.a -lz -lpthread -o $@
++rsem-scan-for-paired-end-reads : sam/bam.h sam/sam.h my_assert.h scanForPairedEndReads.cpp
++	$(CC) $(CFLAGS) scanForPairedEndReads.cpp ${EBROOTSAMTOOLS}/lib/libbam.a -lz -lpthread -o $@
+
+ clean :
+ 	rm -f *.o *~ $(PROGRAMS)
+--- detonate-1.11/ref-eval/Makefile.orig	2016-06-22 23:34:39.000000000 +0200
++++ detonate-1.11/ref-eval/Makefile	2018-01-23 15:10:47.078223944 +0100
+@@ -40,19 +40,19 @@
+
+ CXXFLAGS       = -W -Wno-unused-parameter -g -O3
+ CXXFLAGS_DEBUG = -g3 -fno-inline -O0 -Wall -Wextra 
+-BOOST_INC = -Iboost
+-BOOST_LIB = boost/stage/lib/libboost_program_options.a boost/stage/lib/libboost_random.a
++BOOST_INC = -I${EBROOTBOOST}/include
++BOOST_LIB = ${EBROOTBOOST}/lib/libboost_program_options.a ${EBROOTBOOST}/lib/libboost_random.a
+ LEMON_INC = -Ilemon/build -Ilemon/lemon-main-473c71baff72
+ LEMON_LIB = lemon/build/lemon/libemon.a -lpthread
+ CITY_INC  = -Icity/install/include
+ CITY_LIB  = city/install/lib/libcityhash.a
+ SAM_INC  = -I.
+-SAM_LIB  = sam/libbam.a
+-SH_INC 	  = -Isparsehash/include
++SAM_LIB  = ${EBROOTSAMTOOLS}/lib/libbam.a
++SH_INC 	  = -I${EBROOTSPARSEHASH}/include
+ DL_INC 	  = -Ideweylab
+ INC = $(BOOST_INC) $(LEMON_INC) $(CITY_INC) $(SAM_INC) $(SH_INC) $(DL_INC)
+ LIB = $(BOOST_LIB) $(LEMON_LIB) $(CITY_LIB) $(SAM_LIB)
+-TEST_LIB = boost/stage/lib/libboost_unit_test_framework.a
++TEST_LIB = ${EBROOTBOOST}/lib/libboost_unit_test_framework.a -lboost_system
+
+ ifeq (${NEED_CMAKE}, yes)
+   wd := $(shell pwd)
+@@ -140,7 +140,7 @@
+ 	@echo 
+ 	cd sparsehash && $(MAKE)
+
+-ref-eval: ref-eval.cpp boost/finished lemon/finished city/finished sam/libbam.a sparsehash/finished
++ref-eval: ref-eval.cpp lemon/finished city/finished
+ 	@echo 
+ 	@echo -----------------------------
+ 	@echo - Building REF-EVAL itself. -
+@@ -148,7 +148,7 @@
+ 	@echo 
+ 	$(CXX) $(OMP) $(CXXFLAGS) $(INC) ref-eval.cpp $(LIB) -o ref-eval
+
+-ref-eval-estimate-true-assembly: ref-eval-estimate-true-assembly.cpp boost/finished lemon/finished city/finished sam/libbam.a sparsehash/finished
++ref-eval-estimate-true-assembly: ref-eval-estimate-true-assembly.cpp lemon/finished city/finished
+ 	@echo 
+ 	@echo ---------------------------------------------------
+ 	@echo - Building program to estimate the true assembly. -
+@@ -170,7 +170,7 @@
+ all_tests := test_lazycsv test_line_stream test_blast test_psl test_pairset test_mask test_alignment_segment test_re_matched test_re_kc
+
+ .PHONY: test
+-test: test_msg ${all_tests} boost/finished lemon/finished city/finished sparsehash/finished
++test: test_msg ${all_tests} lemon/finished city/finished
+ 	./test_lazycsv
+ 	./test_line_stream
+ 	./test_blast

easybuild/easyconfigs/d/DETONATE/DETONATE-1.11_include-fix.patch

@@ -0,0 +1,10 @@
+diff -u detonate-1.11/ref-eval/pairset.hh.orig detonate-1.11/ref-eval/pairset.hh
+--- detonate-1.11/ref-eval/pairset.hh.orig	2016-06-22 23:34:39.000000000 +0200
++++ detonate-1.11/ref-eval/pairset.hh	2024-01-08 18:31:58.579745141 +0100
+@@ -21,6 +21,7 @@
+ #include <set>
+ #include <vector>
+ #include <queue>
++#include <list>
+ #include <boost/foreach.hpp>
+ #include <boost/lexical_cast.hpp>

easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.20-GCC-12.3.0.eb

@@ -0,0 +1,29 @@
+name = 'SAMtools'
+version = '0.1.20'
+
+homepage = 'https://www.htslib.org/'
+description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, 
+ including sorting, merging, indexing and generating alignments in a per-position format."""
+
+toolchain = {'name': 'GCC', 'version': '12.3.0'}
+# toolchainopts = {'pic': True}
+
+source_urls = ['https://github.com/%(namelower)s/%(namelower)s/archive/%(version)s']
+sources = [SOURCELOWER_TAR_GZ]
+patches = ['SAMtools-%(version)s_Makefile-ncurses.patch']
+checksums = [
+    {'samtools-0.1.20.tar.gz': '500019b4d1886ad995513d5ce8b413b14b51f16f251ce76bc0b35a446b182a47'},
+    {'SAMtools-0.1.20_Makefile-ncurses.patch': 'f01a05b73f28ff47e816d13a06b27083ec45a3ff93537378affeddf75f614bba'},
+]
+
+# The htslib component of SAMtools >= 1.4 uses zlib, bzip2 and lzma compression.
+# The latter is currently provided by XZ.
+dependencies = [
+    ('ncurses', '6.4'),
+    ('zlib', '1.2.13'),
+    # ('bzip2', '1.0.8'),
+    # ('XZ', '5.4.2'),
+    # ('cURL', '8.0.1'),
+]
+
+moduleclass = 'bio'

easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.4-GCCcore-12.3.0.eb

@@ -0,0 +1,37 @@
+# Updated from previous easyconfig
+# Author: Pavel Grochal (INUITS)
+# Update: Pavel Tománek (INUITS)
+# License: GPLv2
+# Updated to GCCcore-12.3.0 
+# Author: J. Sassmannshausen (Imperial College London/UK)
+
+easyblock = 'ConfigureMake'
+
+name = 'sparsehash'
+version = '2.0.4'
+
+homepage = 'https://github.com/sparsehash/sparsehash'
+description = """
+ An extremely memory-efficient hash_map implementation. 2 bits/entry overhead!
+ The SparseHash library contains several hash-map implementations, including
+ implementations that optimize for space or speed.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = [GITHUB_SOURCE]
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['8cd1a95827dfd8270927894eb77f62b4087735cbede953884647f16c521c7e58']
+
+builddependencies = [
+    ('binutils', '2.40'),
+]
+
+
+sanity_check_paths = {
+    'files': ['include/google/type_traits.h'],
+    'dirs': [],
+}
+
+moduleclass = 'devel'