adding easyconfigs: ABRicate-1.0.0-gompi-2023b.eb, BLAST+-2.16.0-gomp…

…i-2023b.eb, BWA-0.7.18-GCCcore-13.2.0.eb, prokka-1.14.5-gompi-2023b.eb, SKESA-2.4.0-gompi-2023b_saute.1.3.0_2.eb, VCFtools-0.1.16-GCC-13.2.0.eb

easybuild/easyconfigs/a/ABRicate/ABRicate-1.0.0-gompi-2023b.eb

@@ -0,0 +1,41 @@
+# Author: Pavel Grochal (INUITS)
+# License: GPLv2
+
+easyblock = 'Tarball'
+
+name = 'ABRicate'
+version = '1.0.0'
+
+homepage = 'https://github.com/tseemann/abricate'
+description = "Mass screening of contigs for antimicrobial and virulence genes"
+
+toolchain = {'name': 'gompi', 'version': '2023b'}
+
+# https://github.com/tseemann/abricate
+github_account = 'tseemann'
+source_urls = [GITHUB_LOWER_SOURCE]
+sources = ['v%(version)s.zip']
+checksums = ['e7e2af45e47b887c4dba754af87a24014dcb5552eb3fe2a3fd66bb5359a0daf9']
+
+dependencies = [
+    ('Perl', '5.38.0'),
+    ('any2fasta', '0.4.2'),
+    ('BioPerl', '1.7.8'),
+    ('BLAST+', '2.16.0'),
+]
+
+postinstallcmds = ['%(installdir)s/bin/abricate --setupdb']
+
+sanity_check_paths = {
+    'files': ['bin/abricate', 'bin/abricate-get_db'],
+    'dirs': ['db'],
+}
+
+sanity_check_commands = [
+    "abricate --help",
+    "abricate --list",
+]
+
+modloadmsg = "abricate databases are located in $EBROOTABRICATE/db\n"
+
+moduleclass = 'bio'

easybuild/easyconfigs/a/any2fasta/any2fasta-0.4.2-GCCcore-13.2.0.eb

@@ -0,0 +1,35 @@
+# Author: Pavel Grochal (INUITS)
+# Updated by: Denis Kristak (INUITS)
+# License: GPLv2
+
+easyblock = 'Tarball'
+
+name = 'any2fasta'
+version = '0.4.2'
+
+homepage = 'https://github.com/tseemann/any2fasta'
+description = "Convert various sequence formats to FASTA"
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+
+# https://github.com/tseemann/any2fasta
+github_account = 'tseemann'
+source_urls = [GITHUB_SOURCE]
+sources = ['v%(version)s.zip']
+checksums = ['3faa738ab409c7073afe3769e9d32dd5b28a2c12e72c2e4ac6f4e9946ee9a22f']
+
+dependencies = [('Perl', '5.38.0')]
+
+modextrapaths = {'PATH': ''}
+
+sanity_check_paths = {
+    'files': ['any2fasta'],
+    'dirs': [],
+}
+
+sanity_check_commands = [
+    'any2fasta -h',
+    'any2fasta -q %(builddir)s/%(name)s-%(version)s/test.fq',
+]
+
+moduleclass = 'tools'

easybuild/easyconfigs/b/BLAST+/BLAST+-2.16.0-gompi-2023b.eb

@@ -0,0 +1,58 @@
+# #
+# EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+#
+# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA
+# Authors::   Fotis Georgatos <[email protected]>, Kenneth Hoste (UGent)
+# License::   MIT/GPL
+# $Id$
+#
+# This work implements a part of the HPCBIOS project and is a component of
+# the policy: https://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html
+# #
+
+easyblock = 'ConfigureMake'
+
+name = 'BLAST+'
+version = '2.16.0'
+
+homepage = 'https://blast.ncbi.nlm.nih.gov/'
+description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm
+ for comparing primary biological sequence information, such as the amino-acid
+ sequences of different proteins or the nucleotides of DNA sequences."""
+
+toolchain = {'name': 'gompi', 'version': '2023b'}
+toolchainopts = {'usempi': True, 'pic': True}
+
+source_urls = ['https://ftp.ncbi.nlm.nih.gov/blast/executables/%(namelower)s/%(version)s/']
+sources = ['ncbi-blast-%(version)s+-src.tar.gz']
+checksums = ['17c93cf009721023e5aecf5753f9c6a255d157561638b91b3ad7276fd6950c2b']
+
+builddependencies = [('cpio', '2.15')]
+
+dependencies = [
+    ('zlib', '1.2.13'),
+    ('bzip2', '1.0.8'),
+    ('zstd', '1.5.5'),
+    ('PCRE', '8.45'),
+    ('Boost', '1.83.0'),
+    ('GMP', '6.3.0'),
+    ('libpng', '1.6.40'),
+    ('libjpeg-turbo', '3.0.1'),
+    ('LMDB', '0.9.31'),
+    ('SQLite', '3.43.1'),
+]
+
+# remove line that prepends system paths to $PATH from configure script
+preconfigopts = r'sed -i "s|^PATH=\(.*\)$|#PATH=\1 |" %(start_dir)s/src/build-system/configure && '
+
+configopts = "--with-z=$EBROOTZLIB --with-bz2=$EBROOTBZIP2 "
+configopts += "--with-pcre=$EBROOTPCRE --with-boost=$EBROOTBOOST "
+configopts += "--with-gmp=$EBROOTGMP --with-png=$EBROOTLIBPNG "
+configopts += "--with-jpeg=$EBROOTLIBJPEGMINTURBO --with-lmdb=$EBROOTLMDB"
+
+sanity_check_paths = {
+    'files': ['bin/blastn', 'bin/blastp', 'bin/blastx'],
+    'dirs': [],
+}
+
+moduleclass = 'bio'

easybuild/easyconfigs/b/BWA/BWA-0.7.18-GCCcore-13.2.0.eb

@@ -0,0 +1,52 @@
+##
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+#
+# Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA
+# Authors::   George Tsouloupas <[email protected]>, Fotis Georgatos <[email protected]>
+# License::   MIT/GPL
+# $Id$
+#
+# This work implements a part of the HPCBIOS project and is a component of the policy:
+# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html
+#
+# Version >= 0.7.15
+# Author: Adam Huffman
+# The Francis Crick Institute
+#
+# Note that upstream development is mainly at: https://github.com/lh3/bwa
+#
+# 0.7.18
+# Erica Bianco (HPCNow!)
+##
+
+name = 'BWA'
+version = '0.7.18'
+
+homepage = 'http://bio-bwa.sourceforge.net/'
+description = """
+ Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively
+ short nucleotide sequences against a long reference sequence such as the human
+ genome.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://github.com/lh3/%(name)s/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['194788087f7b9a77c0114aa481b2ef21439f6abab72488c83917302e8d0e7870']
+
+builddependencies = [('binutils', '2.40')]
+
+dependencies = [
+    ('zlib', '1.2.13'),
+    ('Perl', '5.38.0'),
+]
+
+# Allow use of x86 intrinsics on PPC
+prebuildopts = 'export CFLAGS="$CFLAGS -fcommon -DNO_WARN_X86_INTRINSICS" && '
+prebuildopts += "sed -i 's|^CC=|#CC=|g' Makefile && "
+prebuildopts += "sed -i 's|^CFLAGS=|#CFLAGS=|g' Makefile && "
+prebuildopts += "sed -i 's|^LIBS=|LIBS= $(LDFLAGS) |g' Makefile && "
+
+moduleclass = 'bio'

easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-13.2.0.eb

@@ -0,0 +1,28 @@
+easyblock = 'PerlModule'
+
+name = 'Bio-SearchIO-hmmer'
+version = '1.7.3'
+
+homepage = 'https://metacpan.org/pod/Bio::SearchIO::hmmer3'
+description = """Code to parse output from hmmsearch, hmmscan, phmmer and nhmmer, compatible
+with both version 2 and version 3 of the HMMER package from http://hmmer.org."""
+
+toolchain = {'name': 'GCC', 'version': '13.2.0'}
+
+source_urls = ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/']
+sources = [SOURCE_TAR_GZ]
+checksums = ['686152f8ce7c611d27ee35ac002ecc309f6270e289a482993796a23bb5388246']
+
+dependencies = [
+    ('Perl', '5.38.0'),
+    ('BioPerl', '1.7.8'),
+]
+
+options = {'modulename': 'Bio::SearchIO::hmmer3'}
+
+sanity_check_paths = {
+    'files': ['bin/bp_%s.pl' % x for x in ['hmmer_to_table', 'parse_hmmsearch']],
+    'dirs': [],
+}
+
+moduleclass = 'bio'

easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2023b.eb

@@ -0,0 +1,50 @@
+# EasyBuild easyconfig
+#
+# John Dey [email protected]
+# Fred Hutchenson Cancer Research Center
+#
+# Updated: Pavel Grochal (INUITS)
+
+easyblock = 'Tarball'
+
+name = 'prokka'
+version = '1.14.5'
+
+homepage = 'https://www.vicbioinformatics.com/software.prokka.shtml'
+description = "Prokka is a software tool for the rapid annotation of prokaryotic genomes."
+
+toolchain = {'name': 'gompi', 'version': '2023b'}
+
+source_urls = ['https://github.com/tseemann/prokka/archive/']
+sources = ['v%(version)s.zip']
+checksums = ['0c13dd5621c352633565f5831c4e85ce2e1e400c2f17ba50800282ae121803ff']
+
+dependencies = [
+    ('BioPerl', '1.7.8'),
+    ('BLAST+', '2.16.0'),
+    ('Java', '11', '', SYSTEM),
+    ('Bio-SearchIO-hmmer', '1.7.3'),
+    ('parallel', '20240322'),
+    ('tbl2asn', '20230713'),
+]
+
+local_bin_files = ['prokka', 'prokka-cdd_to_hmm', 'prokka-genpept_to_fasta_db', 'prokka-tigrfams_to_hmm',
+                   'prokka-biocyc_to_fasta_db', 'prokka-clusters_to_hmm', 'prokka-hamap_to_hmm',
+                   'prokka-uniprot_to_fasta_db', 'prokka-build_kingdom_dbs', 'prokka-genbank_to_fasta_db',
+                   'prokka-make_tarball']
+
+postinstallcmds = ["%(installdir)s/bin/prokka --setupdb"]
+
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in local_bin_files] + ['binaries/linux/aragorn', 'db/cm/Bacteria', 'doc/ToDoList.txt'],
+    'dirs': ['bin', 'binaries', 'db',  'db/cm', 'db/genus', 'db/hmm', 'db/kingdom', 'doc'],
+}
+
+sanity_check_commands = [
+    "prokka --version",
+    "prokka --listdb",
+]
+
+modloadmsg = "prokka scripts are located in $EBROOTPROKKA/bin; databases are located in $EBROOTPROKKA/db\n"
+
+moduleclass = 'bio'

easybuild/easyconfigs/s/SKESA/SKESA-2.4.0-gompi-2023b_saute.1.3.0_2.eb

@@ -0,0 +1,37 @@
+easyblock = 'MakeCp'
+
+name = 'SKESA'
+version = '2.4.0'
+versionsuffix = '_saute.1.3.0_2'
+
+homepage = 'https://github.com/ncbi/SKESA'
+description = "SKESA is a de-novo sequence read assembler for cultured single isolate genomes based on DeBruijn graphs."
+
+toolchain = {'name': 'gompi', 'version': '2023b'}
+toolchainopts = {'cstd': 'c++11'}
+
+source_urls = ['https://github.com/ncbi/SKESA/archive/']
+sources = ['skesa.%(version)s%(versionsuffix)s.tar.gz']
+checksums = ['dc5ad60f963afb09d3f2a3bab8917e657bd93364f0deca6e6844ede44968e979']
+
+dependencies = [
+    ('Boost', '1.83.0'),
+    ('SRA-Toolkit', '3.1.1'),
+    ('ncbi-vdb', '3.1.1'),
+]
+
+prebuildopts = "touch %(builddir)s/ngs.done && "
+
+buildopts = 'CC="$CXX" CFLAGS="$CXXFLAGS" '
+buildopts += "NGS_DIR=%(builddir)s BOOST_PATH=$EBROOTBOOST NGS_PATH=$EBROOTSRAMINTOOLKIT VDB_PATH=$EBROOTNCBIMINVDB"
+
+files_to_copy = [(['skesa'], 'bin')]
+
+sanity_check_paths = {
+    'files': ['bin/skesa'],
+    'dirs': [],
+}
+
+sanity_check_commands = ["skesa --help"]
+
+moduleclass = 'bio'

easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-13.2.0.eb

@@ -0,0 +1,69 @@
+# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/
+# Author: Pablo Escobar Lopez
+# sciCORE - University of Basel
+# SIB Swiss Institute of Bioinformatics
+# revised by Ariel Lozano
+
+easyblock = 'Bundle'
+
+name = 'tbl2asn'
+version = '20230713'
+
+homepage = 'https://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/'
+description = """Tbl2asn is a command-line program that automates the creation of
+ sequence records for submission to GenBank"""
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('patchelf', '0.18.0'),
+]
+
+dependencies = [
+    ('zlib', '1.2.13'),
+]
+
+# libraries that are copied to installdir need to be patched to have an RPATH section
+# when EasyBuild is configured to use RPATH linking (required to pass RPATH sanity check);
+
+default_easyblock = 'CmdCp'
+
+# It is not entirely clean how long NCBI keeps "older" versions. At April 29, 2022, we had six timestamps/versions,
+# reporiting the same verion (tbl2asn --help -> 25.8) but 5 out of 6 (gunzipped) executables have different sha256
+# checksums.
+
+components = [
+    ('libidn', '1.34', {
+        'easyblock': 'ConfigureMake',
+        'source_urls': [GNU_SOURCE],
+        'sources': [SOURCELOWER_TAR_GZ],
+        'start_dir': '%(namelower)s-%(version)s',
+        'checksums': ['3719e2975f2fb28605df3479c380af2cf4ab4e919e1506527e4c7670afff6e3c'],
+    }),
+    (name, version, {
+        'source_urls': ['https://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/versions/%s/all/' %
+                        (version[:4] + '-' + version[4:6] + '-' + version[6:])],
+        'sources': [{'download_filename': 'tbl2asn.linux64.gz',
+                    'filename': '%(name)s-%(version)s%(versionsuffix)s.gz'}],
+        'checksums': ['544c4a2a53f2121fd21c44778fc61980a701ce852ea0142979241c0465c38a0c'],
+        'cmds_map': [('.*', "cp %(name)s-%(version)s%(versionsuffix)s tbl2asn")],
+        'files_to_copy': [(['tbl2asn'], 'bin')],
+    }),
+]
+
+postinstallcmds = [
+    "if %(rpath_enabled)s; then "
+    "  patchelf --force-rpath --set-rpath %(installdir)s/lib %(installdir)s/bin/tbl2asn;"
+    "fi",
+    "chmod +x %(installdir)s/bin/tbl2asn",
+]
+
+sanity_check_paths = {
+    'files': ['bin/tbl2asn', 'bin/idn', 'lib/libidn.%s' % SHLIB_EXT],
+    'dirs': ['include'],
+}
+
+sanity_check_commands = ['tbl2asn --help']
+
+moduleclass = 'bio'