VEP and freebayes (and deps)

easyconfigs/f/fastahack/fastahack-1.0.0-GCCcore-12.2.0.eb

@@ -0,0 +1,36 @@
+# Updated: Denis Kristak (INUITS)
+# Updated: Petr Král (INUITS)
+
+easyblock = 'ConfigureMake'
+
+name = 'fastahack'
+version = '1.0.0'
+
+homepage = 'https://github.com/ekg/fastahack'
+description = """Utilities for indexing and sequence extraction from FASTA files."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+
+github_account = 'ekg'
+source_urls = [GITHUB_SOURCE]
+sources = ['v%(version)s.tar.gz']
+patches = ['%(name)s-%(version)s_build-libs.patch']
+checksums = [
+    'cc1c04729b0c8ba3647cbb7e15e2b490ce701d73773f30f5892d68c36a1dceae',  # v1.0.0.tar.gz
+    '7f804486c6bafd9b1572cb5f86ff28dbebb4d6da551bde1091d6ff8f82748bf4',  # fastahack-1.0.0_build-libs.patch
+]
+
+builddependencies = [('binutils', '2.39')]
+
+skipsteps = ['configure']
+
+installopts = 'PREFIX=%(installdir)s '
+
+sanity_check_paths = {
+    'files': ['bin/%(name)s', 'lib/libfastahack.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+sanity_check_commands = ['%(name)s --help']
+
+moduleclass = 'bio'

easyconfigs/f/fermi-lite/fermi-lite-20190320-GCCcore-12.2.0.eb

@@ -0,0 +1,48 @@
+# Author: Jasper Grimm (UoY)
+
+easyblock = 'MakeCp'
+
+name = 'fermi-lite'
+version = '20190320'
+local_commit = 'b499514'
+
+homepage = 'https://github.com/lh3/fermi-lite'
+description = """Standalone C library for assembling Illumina short reads in small regions."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+
+github_account = 'lh3'
+source_urls = [GITHUB_SOURCE]
+sources = ['%s.tar.gz' % local_commit]
+patches = [
+    '%(name)s-20190320_avoid-bwa-namespace-conflict.patch',
+    '%(name)s-20190320_build-shared-lib.patch',
+]
+checksums = [
+    'ea1230e298b8e7193a996b5aceeff7fea44ef00852b0b87d4fcb504bdca0e712',  # b499514.tar.gz
+    # fermi-lite-20190320_avoid-bwa-namespace-conflict.patch
+    '27600733f1cea8b1d1503b1a67b9d41526e907c1b6321313ff51194e166c1842',
+    '43398559fbb3910d6d3d1a41af3fb16bf8f26bd7cc34176dfc9a068a551c3f50',  # fermi-lite-20190320_build-shared-lib.patch
+]
+
+builddependencies = [('binutils', '2.39')]
+
+dependencies = [('zlib', '1.2.12')]
+
+prebuildopts = 'CFLAGS="$CFLAGS -fcommon"'
+
+parallel = 1
+
+files_to_copy = [
+    (['fml-asm'], 'bin'),
+    (['*.a', '*.%s*' % SHLIB_EXT], 'lib'),
+    (['*.h'], 'include/fml'),
+    'test',
+]
+
+sanity_check_paths = {
+    'files': ['bin/fml-asm', 'lib/libfml.a', 'lib/libfml.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+moduleclass = 'bio'

easyconfigs/f/filevercmp/filevercmp-20191210-GCCcore-12.2.0.eb

@@ -0,0 +1,37 @@
+# Updated: Denis Kristak (INUITS)
+# Updated: Petr Král (INUITS)
+
+easyblock = 'ConfigureMake'
+
+name = 'filevercmp'
+version = '20191210'
+local_commit = 'df20dcc'
+
+homepage = 'https://github.com/ekg/filevercmp'
+description = """filevercmp function as in sort --version-sort."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+
+github_account = 'ekg'
+source_urls = [GITHUB_SOURCE]
+sources = ['%s.tar.gz' % local_commit]
+patches = ['%(name)s-%(version)s_build-libs.patch']
+checksums = [
+    '89835829a7829f7a25783b2cf9d482f1e3c794703343c9214c15c66a8c7f4aae',  # df20dcc.tar.gz
+    '051438f76dd04219abfb283f61101c04d748407031e180b7ae3841344416ec4f',  # filevercmp-20191210_build-libs.patch
+]
+
+builddependencies = [('binutils', '2.39')]
+
+skipsteps = ['configure']
+
+installopts = 'DESTDIR="" PREFIX=%(installdir)s '
+
+sanity_check_paths = {
+    'files': ['bin/%(name)s', 'lib/libfilevercmp.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+sanity_check_commands = ['%(name)s abca bcac']
+
+moduleclass = 'lib'

easyconfigs/f/freebayes/freebayes-1.3.8-foss-2022b-R-4.3.1.eb

@@ -0,0 +1,52 @@
+easyblock = 'MesonNinja'
+
+name = 'freebayes'
+version = '1.3.8'
+versionsuffix = '-R-%(rver)s'
+
+homepage = 'https://github.com/freebayes/freebayes'
+description = "Bayesian haplotype-based genetic polymorphism discovery and genotyping."
+
+toolchain = {'name': 'foss', 'version': '2022b'}
+
+source_urls = [GITHUB_SOURCE]
+sources = ['v%(version)s.tar.gz']
+patches = [
+    '%(name)s-1.3.8_fix-meson.patch',
+    '%(name)s-1.3.8_fix-includes.patch',
+]
+checksums = [
+    {'v1.3.8.tar.gz': 'd1c24b1d1b35277e7403cd67063557998218a105c916b01a745e7704715fce67'},
+    {'freebayes-1.3.8_fix-meson.patch': 'c5064f0e50aa508875f56bce3e4c5df5520c6a9330bbcd25abfbe28d38d9415f'},
+    {'freebayes-1.3.8_fix-includes.patch': '7d2439824a674e81830069fba2d0d325231cf173c0c47503043c4b5290bafe83'},
+]
+
+builddependencies = [
+    ('CMake', '3.24.3'),
+    ('Meson', '0.64.0'),
+    ('Ninja', '1.11.1'),
+    ('pkgconf', '1.9.3'),
+]
+
+dependencies = [
+    ('Python', '3.10.8'),
+    ('R', '4.3.1'),
+    ('parallel', '20230722'),
+    ('libffi', '3.4.4'),
+    ('VCFtools', '0.1.16'),
+    ('vcflib', '1.0.9', versionsuffix),
+    ('SeqLib', '1.2.0'),
+]
+
+configopts = "-Dprefer_system_deps=true --buildtype release"
+
+sanity_check_paths = {
+    'files': ['bin/freebayes', 'bin/bamleftalign', 'scripts/freebayes-parallel'],
+    'dirs': [],
+}
+
+sanity_check_commands = ["freebayes --help"]
+
+modextrapaths = {'PATH': ['scripts']}
+
+moduleclass = 'bio'

easyconfigs/f/freebayes/freebayes-1.3.8_fix-includes.patch

@@ -0,0 +1,170 @@
+diff -aur src.old/Allele.cpp src/Allele.cpp
+--- src.old/Allele.cpp	2023-11-02 11:22:34.796332342 +0000
++++ src/Allele.cpp	2023-11-02 11:24:32.703959281 +0000
+@@ -1,5 +1,5 @@
+ #include "Allele.h"
+-#include "multichoose.h"
++#include "multichoose/multichoose.h"
+ #include "TryCatch.h"
+
+
+diff -aur src.old/AlleleParser.cpp src/AlleleParser.cpp
+--- src.old/AlleleParser.cpp	2023-11-02 11:22:34.796332342 +0000
++++ src/AlleleParser.cpp	2023-11-02 11:25:12.378171715 +0000
+@@ -1,9 +1,9 @@
+ #include "AlleleParser.h"
+-#include "multichoose.h" // includes generic functions, so it must be included here
++#include "multichoose/multichoose.h" // includes generic functions, so it must be included here
+                          // otherwise we will get a linker error
+                          // see: http://stackoverflow.com/questions/36039/templates-spread-across-multiple-files
+                          // http://www.cplusplus.com/doc/tutorial/templates/ "Templates and Multi-file projects"
+-#include "multipermute.h"
++#include "multichoose/multipermute.h"
+ #include "Logging.h"
+
+ using namespace std;
+diff -aur src.old/AlleleParser.h src/AlleleParser.h
+--- src.old/AlleleParser.h	2023-11-02 11:22:34.796332342 +0000
++++ src/AlleleParser.h	2023-11-02 11:25:38.524311709 +0000
+@@ -13,7 +13,7 @@
+ #include <assert.h>
+ #include <ctype.h>
+ #include <cmath>
+-#include "split.h"
++#include "fastahack/split.h"
+ #include <list> // XXX workaround for a missing include in vcflib's join.h
+ #include "join.h"
+
+diff -aur src.old/BedReader.cpp src/BedReader.cpp
+--- src.old/BedReader.cpp	2023-11-02 11:22:34.796332342 +0000
++++ src/BedReader.cpp	2023-11-02 11:26:21.545542054 +0000
+@@ -7,11 +7,11 @@
+ #include <iterator>
+ #include <algorithm>
+ #include <cmath>
+-#include "split.h"
++#include "fastahack/split.h"
+ #include "Utility.h"
+ #include "BedReader.h"
+ #include "Logging.h"
+-#include <IntervalTree.h>
++#include "intervaltree/IntervalTree.h"
+
+ using namespace std;
+
+diff -aur src.old/BedReader.h src/BedReader.h
+--- src.old/BedReader.h	2023-11-02 11:22:34.796332342 +0000
++++ src/BedReader.h	2023-11-02 11:38:46.992500997 +0000
+@@ -9,8 +9,8 @@
+ #include <map>
+ #include <iterator>
+ #include <algorithm>
+-#include <IntervalTree.h>
+-#include "split.h"
++#include "intervaltree/IntervalTree.h"
++#include "fastahack/split.h"
+
+ using namespace std;
+
+diff -aur src.old/Bias.h src/Bias.h
+--- src.old/Bias.h	2023-11-02 11:22:34.796332342 +0000
++++ src/Bias.h	2023-11-02 11:39:09.840622964 +0000
+@@ -7,7 +7,7 @@
+ #include <string>
+ #include <vector>
+ #include <cstdlib>
+-#include "split.h"
++#include "fastahack/split.h"
+
+ using namespace std;
+
+diff -aur src.old/CNV.h src/CNV.h
+--- src.old/CNV.h	2023-11-02 11:22:34.796332342 +0000
++++ src/CNV.h	2023-11-02 11:39:32.400743396 +0000
+@@ -10,7 +10,7 @@
+ #include <stdlib.h>
+ #include <algorithm>
+ #include <tuple>
+-#include "split.h"
++#include "fastahack/split.h"
+
+ using namespace std;
+
+diff -aur src.old/Contamination.h src/Contamination.h
+--- src.old/Contamination.h	2023-11-02 11:22:34.796332342 +0000
++++ src/Contamination.h	2023-11-02 11:39:58.004880079 +0000
+@@ -8,7 +8,7 @@
+ #include <vector>
+ #include <cstdlib>
+ #include <cmath>
+-#include "split.h"
++#include "fastahack/split.h"
+
+ using namespace std;
+
+diff -aur src.old/DataLikelihood.cpp src/DataLikelihood.cpp
+--- src.old/DataLikelihood.cpp	2023-11-02 11:22:34.796332342 +0000
++++ src/DataLikelihood.cpp	2023-11-02 11:40:49.070152682 +0000
+@@ -1,6 +1,6 @@
+ #include "DataLikelihood.h"
+-#include "multichoose.h"
+-#include "multipermute.h"
++#include "multichoose/multichoose.h"
++#include "multichoose/multipermute.h"
+ #include "Logging.h"
+
+ long double
+diff -aur src.old/FBFasta.h src/FBFasta.h
+--- src.old/FBFasta.h	2023-11-02 11:22:34.796332342 +0000
++++ src/FBFasta.h	2023-11-02 11:42:06.352565235 +0000
+@@ -16,10 +16,10 @@
+ #include <stdint.h>
+ #include <stdio.h>
+ #include <algorithm>
+-#include "LargeFileSupport.h"
++#include "fastahack/LargeFileSupport.h"
+ #include "Utility.h"
+ #include <sys/stat.h>
+-#include "split.h"
++#include "fastahack/split.h"
+ #include <stdlib.h>
+ #include <ctype.h>
+ #include <unistd.h>
+diff -aur src.old/freebayes.cpp src/freebayes.cpp
+--- src.old/freebayes.cpp	2023-11-02 11:22:34.797332347 +0000
++++ src/freebayes.cpp	2023-11-02 11:48:20.423563787 +0000
+@@ -30,8 +30,8 @@
+ #include "Utility.h"
+ #include "SegfaultHandler.h"
+
+-#include "multichoose.h"
+-#include "multipermute.h"
++#include "multichoose/multichoose.h"
++#include "multichoose/multipermute.h"
+
+ #include "Genotype.h"
+ #include "DataLikelihood.h"
+diff -aur src.old/Genotype.cpp src/Genotype.cpp
+--- src.old/Genotype.cpp	2023-11-02 11:22:34.796332342 +0000
++++ src/Genotype.cpp	2023-11-02 11:48:46.936705835 +0000
+@@ -1,6 +1,6 @@
+ #include "Genotype.h"
+-#include "multichoose.h"
+-#include "multipermute.h"
++#include "multichoose/multichoose.h"
++#include "multichoose/multipermute.h"
+
+
+ vector<Allele*> Genotype::uniqueAlleles(void) {
+diff -aur src.old/Parameters.h src/Parameters.h
+--- src.old/Parameters.h	2023-11-02 11:22:34.796332342 +0000
++++ src/Parameters.h	2023-11-02 11:49:13.701849229 +0000
+@@ -9,7 +9,7 @@
+ #include <map>
+ #include <getopt.h>
+ #include <stdlib.h>
+-#include "split.h"
++#include "fastahack/split.h"
+ #include "version_git.h"
+ #include "Utility.h"
+