diff --git a/271_phyluce/ABySS-2.3.7-foss-2023a.eb b/271_phyluce/ABySS-2.3.7-foss-2023a.eb deleted file mode 100644 index b7ed9556..00000000 --- a/271_phyluce/ABySS-2.3.7-foss-2023a.eb +++ /dev/null @@ -1,34 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'ABySS' -version = '2.3.7' - -homepage = 'https://www.bcgsc.ca/platform/bioinfo/software/abyss' -description = """Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler""" - -toolchain = {'name': 'foss', 'version': '2023a'} -toolchainopts = {'usempi': True, 'cstd': 'c++17'} - -source_urls = ['http://github.com/bcgsc/abyss/releases/download/%(version)s/'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['ba37780e79ec3aa359b6003e383caef13479a87f4d0022af01b86398f9ffca1f'] - -dependencies = [ - ('Autoconf', '2.71'), - ('Automake', '1.16.5'), - ('Boost', '1.82.0'), - ('sparsehash', '2.0.4'), - ('btllib', '1.7.0'), -] - -preconfigopts = "./autogen.sh && " -configopts = 'CXXFLAGS="$CXXFLAGS -Wno-error"' - -sanity_check_paths = { - 'files': ["bin/ABYSS", "bin/ABYSS-P"], - 'dirs': [] -} - -sanity_check_commands = ['ABYSS --help'] - -moduleclass = 'bio' diff --git a/271_phyluce/LASTZ-1.04.22-foss-2023a.eb b/271_phyluce/LASTZ-1.04.22-foss-2023a.eb deleted file mode 100644 index bd9b31a1..00000000 --- a/271_phyluce/LASTZ-1.04.22-foss-2023a.eb +++ /dev/null @@ -1,29 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'LASTZ' -version = '1.04.22' - -homepage = 'https://github.com/lastz/lastz' -description = """ LASTZ is a program for aligning DNA sequences, a pairwise aligner. Originally designed to handle - sequences the size of human chromosomes and from different species, it is also useful for sequences produced by NGS - sequencing technologies such as Roche 454. -""" - -toolchain = {'name': 'GCC', 'version': '12.3.0'} - -source_urls = [GITHUB_LOWER_SOURCE] -sources = ['%(version)s.tar.gz'] -checksums = ['4c829603ba4aed7ddf64255b528cd88850e4557382fca29580d3576c25c5054a'] - -skipsteps = ['configure'] - -buildopts = "allowBackToBackGaps=ON" - -installopts = 'installDir=%(installdir)s/bin' - -sanity_check_paths = { - 'files': ['bin/lastz', 'bin/lastz_D'], - 'dirs': [], -} - -moduleclass = 'bio' diff --git a/271_phyluce/Pilon-1.23-Java-11-wrapped.eb b/271_phyluce/Pilon-1.23-Java-11-wrapped.eb deleted file mode 100644 index 6381fde7..00000000 --- a/271_phyluce/Pilon-1.23-Java-11-wrapped.eb +++ /dev/null @@ -1,33 +0,0 @@ -easyblock = 'JAR' - -name = 'Pilon' -version = '1.23' -versionsuffix = '-Java-%(javaver)s' - -homepage = 'https://github.com/broadinstitute/pilon' -description = " Pilon is an automated genome assembly improvement and variant detection tool" - -toolchain = SYSTEM - -source_urls = ['https://github.com/broadinstitute/pilon/releases/download/v%(version)s/'] -sources = ['pilon-%(version)s.jar'] -checksums = ['bde1d3c8da5537abbc80627f0b2a4165c2b68551690e5733a6adf62413b87185'] - -dependencies = [('Java', '11')] - -sanity_check_paths = { - 'files': ['bin/pilon', 'pilon.jar'], - 'dirs': [], -} - -sanity_check_commands = ["pilon --help"] - -postinstallcmds = [ - "cd %(installdir)s && ln -s %(namelower)s-%(version)s.jar pilon.jar", - "mkdir -p %(installdir)s/bin", - "echo '#!/bin/sh' > %(installdir)s/bin/%(namelower)s", - "echo 'java -jar -Xmx8G %(installdir)s/%(namelower)s-%(version)s.jar $@' >> %(installdir)s/bin/%(namelower)s", - "chmod a+rx %(installdir)s/bin/%(namelower)s" -] - -moduleclass = 'bio' diff --git a/271_phyluce/SPAdes-3.15.4-GCC-12.3.0.eb b/271_phyluce/SPAdes-3.15.4-GCC-12.3.0.eb deleted file mode 100644 index 63a20e12..00000000 --- a/271_phyluce/SPAdes-3.15.4-GCC-12.3.0.eb +++ /dev/null @@ -1,48 +0,0 @@ -# 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 -# Modified by: -# Adam Huffman -# The Francis Crick Institute -# Updated by: -# Filip Kružík (INUITS) -# Pavel Tománek (INUIS) - -easyblock = 'CMakeMake' - -name = 'SPAdes' -version = '3.15.4' - -homepage = 'https://cab.spbu.ru/software/spades/' -description = "Genome assembler for single-cell and isolates data sets" - -toolchain = {'name': 'GCC', 'version': '12.3.0'} - -source_urls = ['http://cab.spbu.ru/files/release%(version)s'] -sources = [SOURCE_TAR_GZ] -checksums = ['3b241c528a42a8bdfdf23e5bf8f0084834790590d08491decea9f0f009d8589f'] - -builddependencies = [ - ('CMake', '3.26.3'), -] -dependencies = [ - ('Python', '3.11.3'), - ('zlib', '1.2.13'), - ('bzip2', '1.0.8'), - ('libreadline', '8.2'), -] - -start_dir = 'src' - -configopts = " -DBoost_NO_BOOST_CMAKE=ON" - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['spades-bwa', 'spades-core', 'spades-gbuilder', 'spades-hammer', - 'spades-ionhammer', 'spades-kmercount', 'spades.py']], - 'dirs': [], -} - -sanity_check_commands = [('%(namelower)s.py', '--test')] - -moduleclass = 'bio' diff --git a/271_phyluce/Velvet-1.2.10-foss-2023a-mt-kmer_191.eb b/271_phyluce/Velvet-1.2.10-foss-2023a-mt-kmer_191.eb deleted file mode 100644 index 3b712ec8..00000000 --- a/271_phyluce/Velvet-1.2.10-foss-2023a-mt-kmer_191.eb +++ /dev/null @@ -1,35 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# -# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA, 2012-2013 The Cyprus Institute -# Authors:: Cedric Laczny , Fotis Georgatos , -# Thekla Loizou , Andreas Panteli -# 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 -## - -name = 'Velvet' -version = '1.2.10' -versionsuffix = '-mt-kmer_191' - -homepage = 'https://github.com/dzerbino/velvet/' -description = """Sequence assembler for very short reads""" - -toolchain = {'name': 'foss', 'version': '2023a'} -toolchainopts = {'openmp': True, 'pic': True} - -github_account = 'dzerbino' -source_urls = [GITHUB_LOWER_SOURCE] -sources = ['v%(version)s.tar.gz'] -checksums = ['4615e52dc2e8a05f1009daf2c0978c218860be364afa044f73677cd298f10c7b'] - -dependencies = [('zlib', '1.2.13')] - -buildopts = "OPENMP=1 MAXKMERLENGTH=%s LONGSEQUENCES=1" % versionsuffix.split('_')[1] - -postinstallcmds = ["cd contrib/MetaVelvet-1.* && make && cd ../../ && cp -a contrib %(installdir)s/"] - -moduleclass = 'bio' diff --git a/271_phyluce/btllib-1.7.0-GCC-12.3.0.eb b/271_phyluce/btllib-1.7.0-GCC-12.3.0.eb deleted file mode 100644 index 960f1b09..00000000 --- a/271_phyluce/btllib-1.7.0-GCC-12.3.0.eb +++ /dev/null @@ -1,43 +0,0 @@ -easyblock = 'CmdCp' - -name = 'btllib' -version = '1.7.0' - -homepage = 'https://github.com/bcgsc/btllib' -description = """Bioinformatics Technology Lab common code library""" - -toolchain = {'name': 'GCC', 'version': '12.3.0'} -toolchainopts = {'openmp': True} - -sources = [{ - 'filename': '%(name)s-%(version)s.tar.gz', - 'git_config': { - 'url': 'https://github.com/bcgsc', - 'repo_name': 'btllib', - 'tag': 'v%(version)s', - 'recursive': True, - 'keep_git_dir': True, - } -}] -checksums = [None] - -dependencies = [ - ('Python', '3.11.3'), - ('Meson', '1.1.1'), - ('Ninja', '1.11.1'), - ('CMake', '3.26.3'), - ('SAMtools', '1.18'), -] - -cmds_map = [('.*', "./compile")] - -files_to_copy = [(['install/bin/*'], 'bin'), (['install/lib/*'], 'lib'), (['install/include/*'], 'include')] - -sanity_check_paths = { - 'files': ['bin/randseq', 'bin/indexlr', 'bin/mi_bf_generate'], - 'dirs': [], -} - -sanity_check_commands = ['randseq --help', 'indexlr --help'] - -moduleclass = 'lang' diff --git a/271_phyluce/bx-python-0.10.0-foss-2023a.eb b/271_phyluce/bx-python-0.10.0-foss-2023a.eb deleted file mode 100644 index da5a1cb4..00000000 --- a/271_phyluce/bx-python-0.10.0-foss-2023a.eb +++ /dev/null @@ -1,34 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'bx-python' -version = '0.10.0' - -homepage = 'https://github.com/bxlab/bx-python' -description = """The bx-python project is a Python library and associated set of scripts to allow for rapid - implementation of genome scale analyses.""" - -toolchain = {'name': 'foss', 'version': '2023a'} - -dependencies = [ - ('Python', '3.11.3'), - ('LZO', '2.10'), - ('SciPy-bundle', '2023.07'), -] - -use_pip = True - -exts_list = [ - ('python-lzo', '1.15', { - 'modulename': 'lzo', - 'preinstallopts': "export PREFIX=$EBROOTLZO && ", - 'checksums': ['a57aaa00c5c3a0515dd9f7426ba2cf601767dc19dc023d8b99d4a13b0a327b49'], - }), - (name, version, { - 'modulename': 'bx', - 'checksums': ['bfe9541d7b18a98e907b085e31f58d3989fbca4dc667c4ae48c33b753e0e2da8'], - }), -] - -sanity_pip_check = True - -moduleclass = 'bio' diff --git a/271_phyluce/error_log.txt b/271_phyluce/error_log.txt deleted file mode 100644 index 5a5b942a..00000000 --- a/271_phyluce/error_log.txt +++ /dev/null @@ -1,36 +0,0 @@ -Error during run Abyss: -ERROR_1: -mpicxx -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I/tmp/vsc47063/easybuild/build/ABySS/2.3.7/foss-2023a/abyss-2.3.7 -I/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-amper-12.3.0/include -I/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/OpenMPI/4.1.5-GCC-12.3.0/include -I/scratch/gent/vo/001/gelake-ampere-ib/software/sparsehash/2.0.4-GCCcore-12.3.0/include -I/apps/gent/RHEL8/cascadelake-ib/software/Boost/1.82.0-GCC-12.3.0/include -I/scratch/gRHEL8/cascadelake-ampere-ib/software/FFTW.MPI/3.3.10-gompi-2023a/include -I/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.3.1-GCC-12.3.0/include -ib/software/FlexiBLAS/3.3.1-GCC-12.3.0/include/flexiblas -isystem/tmp/vsc47063/easybuild/build/ABySS/2.3.7/foss-2023a/abyss-2.3.7/boost_1_56_0 -Wall -Wedeclarations -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -O2 -ftree-vectorize -march=native -fno-math-errno -Wno-error=deprect_a-RUtils.Tpo .deps/libralgorithmsshort_a-RUtils.Po -mv -f .deps/libralgorithmsshort_a-RUtils.Tpo .deps/libralgorithmsshort_a-RUtils.Po -In file included from /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/btllib/1.7.0-GCC-12.3.0/include/btllib/nthash.hpp:12, - from /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/btllib/1.7.0-GCC-12.3.0/include/btllib/bloom_filter.hpp:4, - from BloomFilters.h:4, - from RAlgorithmsShort.h:4, - from RResolverShort.cpp:7: -/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/btllib/1.7.0-GCC-12.3.0/include/btllib/hashing_internals.hpp:554:11: error: -ilable with -std=c++17 or -std=gnu++17 [-Werror=c++17-extensions] - 554 | constexpr inline uint64_t AA_SEED_A = 0xf56d6192468323df; - | ^~~~~~ -/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/btllib/1.7.0-GCC-12.3.0/include/btllib/hashing_internals.hpp:555:11: error: -ilable with -std=c++17 or -std=gnu++17 [-Werror=c++17-extensions] - 555 | constexpr inline uint64_t AA_SEED_C = 0x9b0b2fd724e1e1d2; - | ^~~~~~ -/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/btllib/1.7.0-GCC-12.3.0/include/btllib/hashing_internals.hpp:556:11: error: -ilable with -std=c++17 or -std=gnu++17 [-Werror=c++17-extensions] - 556 | constexpr inline uint64_t AA_SEED_D = 0xe8c583296b03c7af; -..... -mv -f .deps/libralgorithmsshort_a-SequenceTree.Tpo .deps/libralgorithmsshort_a-SequenceTree.Po -cc1plus: all warnings being treated as errors -make[2]: *** [Makefile:555: abyss_rresolver_short-RResolverShort.o] Error 1 -make[2]: *** Waiting for unfinished jobs.... -cc1plus: all warnings being treated as errors -make[2]: *** [Makefile:499: libralgorithmsshort_a-BloomFilters.o] Error 1 -mv -f .deps/abyss_rresolver_short-Contigs.Tpo .deps/abyss_rresolver_short-Contigs.Po -mv -f .deps/libralgorithmsshort_a-Contigs.Tpo .deps/libralgorithmsshort_a-Contigs.Po -cc1plus: all warnings being treated as errors -make[2]: *** [Makefile:485: libralgorithmsshort_a-RAlgorithmsShort.o] Error 1 -make[2]: Leaving directory '/tmp/vsc47063/easybuild/build/ABySS/2.3.7/foss-2023a/abyss-2.3.7/RResolver' -make[1]: *** [Makefile:488: all-recursive] Error 1 -make[1]: Leaving directory '/tmp/vsc47063/easybuild/build/ABySS/2.3.7/foss-2023a/abyss-2.3.7' -make: *** [Makefile:408: all] Error 2 - (at easybuild/easybuild-framework/easybuild/tools/run.py:682 in parse_cmd_output) \ No newline at end of file diff --git a/271_phyluce/phyluce-1.7.3-foss-2023a.eb b/271_phyluce/phyluce-1.7.3-foss-2023a.eb deleted file mode 100644 index 3457960e..00000000 --- a/271_phyluce/phyluce-1.7.3-foss-2023a.eb +++ /dev/null @@ -1,138 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'phyluce' -version = '1.7.3' - -homepage = 'https://github.com/faircloth-lab/phyluce' -description = """ -phyluce is a software package for working with data generated from sequence capture of UCE -(ultra-conserved element) loci, as first published in [BCF2012]. Specifically, phyluce is a suite of programs to: -1) assemble raw sequence reads from Illumina platforms into contigs -2) determine which contigs represent UCE loci -3) filter potentially paralagous UCE loci -4) generate different sets of UCE loci across taxa of interest -""" - -toolchain = {'name': 'foss', 'version': '2023a'} - -dependencies = [ - ('Python', '3.11.3'), - ('Biopython', '1.83'), - ('Python-bundle-PyPI', '2023.06'), - ('snakemake', '8.4.2'), - ('DendroPy', '4.6.1'), - ('bx-python', '0.10.0'), - ('ABySS', '2.3.7'), - ('BCFtools', '1.18'), - ('BEDTools', '2.31.0'), - ('BWA', '0.7.17'), - ('Gblocks', '0.91b', '', SYSTEM), - ('LASTZ', '1.04.22'), - ('MAFFT', '7.520', '-with-extensions'), - ('MUSCLE', '5.1.0'), - ('Pilon', '1.23', '-Java-11-wrapped', SYSTEM), - ('RAxML-NG', '1.2.0'), - ('SAMtools', '1.18'), - ('seqtk', '1.4'), - ('SPAdes', '3.15.4'), - ('trimAl', '1.4.1'), - ('Velvet', '1.2.10', '-mt-kmer_191') -] - -exts_list = [ - (name, version, { - 'source_urls': ['https://github.com/faircloth-lab/phyluce/archive/refs/tags/'], - 'sources': ['v%(version)s.tar.gz'], - 'patches': [ - '%(name)s-%(version)s_fix-config-paths.patch', - '%(name)s-%(version)s_removal-Bio-Alphabet.patch', - ], - 'checksums': [ - {'v1.7.3.tar.gz': '931fd512730bb101266b27728576df00277858d256e1ab30d64b474588362e11'}, - {'phyluce-1.7.3_fix-config-paths.patch': - '22d5467d7498a9b2b718660e9580fb41986964e122e4c3baf851a324a968ae5d'}, - {'phyluce-1.7.3_removal-Bio-Alphabet.patch': - '9401f8b8052924476d2a73d8ac2672e750eadf11618c672d9679f3c99234049d'}, - ], - }), -] - -use_pip = True -sanity_pip_check = True - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -sanity_check_commands = ["%s --help" % x for x in [ - "phyluce_align_extract_taxa_from_alignments", - "phyluce_align_extract_taxon_fasta_from_alignments", - "phyluce_align_filter_alignments", - "phyluce_align_format_concatenated_phylip_for_paml", - "phyluce_align_get_align_summary_data", - "phyluce_align_get_gblocks_trimmed_alignments_from_untrimmed", - "phyluce_align_get_incomplete_matrix_estimates", - "phyluce_align_get_informative_sites", - "phyluce_align_get_only_loci_with_min_taxa", - "phyluce_align_get_ry_recoded_alignments", - "phyluce_align_get_smilogram_from_alignments", - "phyluce_align_get_taxon_locus_counts_in_alignments", - "phyluce_align_get_trimal_trimmed_alignments_from_untrimmed", - "phyluce_align_move_align_by_conf_file", - "phyluce_align_randomly_sample_and_concatenate", - "phyluce_align_reduce_alignments_with_raxml", - "phyluce_align_remove_empty_taxa", - "phyluce_align_remove_locus_name_from_files", - "phyluce_align_screen_alignments_for_problems", - "phyluce_align_seqcap_align", - "phyluce_align_split_concat_nexus_to_loci", - "phyluce_assembly_assemblo_abyss", - "phyluce_assembly_assemblo_spades", - "phyluce_assembly_assemblo_velvet", - "phyluce_assembly_explode_get_fastas_file", - "phyluce_assembly_extract_contigs_to_barcodes", - "phyluce_assembly_get_bed_from_lastz", - "phyluce_assembly_get_fasta_lengths", - "phyluce_assembly_get_fastas_from_match_counts", - "phyluce_assembly_get_fastq_lengths", - "phyluce_assembly_get_match_counts", - "phyluce_assembly_match_contigs_to_barcodes", - "phyluce_genetrees_get_mean_bootrep_support", - "phyluce_genetrees_generate_multilocus_bootstrap_count", - "phyluce_genetrees_rename_tree_leaves", - "phyluce_genetrees_sort_multilocus_bootstraps", - "phyluce_genetrees_get_tree_counts", - "phyluce_ncbi_chunk_fasta_for_ncbi", - "phyluce_ncbi_prep_uce_align_files_for_ncbi", - "phyluce_probe_easy_lastz", - "phyluce_probe_get_genome_sequences_from_bed", - "phyluce_probe_get_locus_bed_from_lastz_files", - "phyluce_probe_get_multi_fasta_table", - "phyluce_probe_get_multi_merge_table", - "phyluce_probe_get_probe_bed_from_lastz_files", - "phyluce_probe_get_screened_loci_by_proximity", - "phyluce_probe_get_subsets_of_tiled_probes", - "phyluce_probe_get_tiled_probe_from_multiple_inputs", - "phyluce_probe_get_tiled_probes", - "phyluce_probe_query_multi_fasta_table", - "phyluce_probe_query_multi_merge_table", - "phyluce_probe_reconstruct_uce_from_probe", - "phyluce_probe_remove_duplicate_hits_from_probes_using_lastz", - "phyluce_probe_remove_overlapping_probes_given_config", - "phyluce_probe_run_multiple_lastzs_sqlite", - "phyluce_probe_slice_sequence_from_genomes", - "phyluce_probe_strip_masked_loci_from_set", - "phyluce_utilities_combine_reads", - "phyluce_utilities_filter_bed_by_fasta", - "phyluce_utilities_get_bed_from_fasta", - "phyluce_utilities_merge_multiple_gzip_files", - "phyluce_utilities_merge_next_seq_gzip_files", - "phyluce_utilities_replace_many_links", - "phyluce_utilities_unmix_fasta_reads", - "phyluce_workflow", -]] - -modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages/phyluce'} - -moduleclass = 'bio' diff --git a/271_phyluce/phyluce-1.7.3_fix-config-paths.patch b/271_phyluce/phyluce-1.7.3_fix-config-paths.patch deleted file mode 100644 index 1d0cbcdb..00000000 --- a/271_phyluce/phyluce-1.7.3_fix-config-paths.patch +++ /dev/null @@ -1,53 +0,0 @@ -fix path of binaries in config file -author: Pavel Tomanek (INUITS) ---- config/phyluce.conf.orig 2024-02-01 11:38:15.279943701 +0100 -+++ config/phyluce.conf 2024-02-01 14:52:31.565662528 +0100 -@@ -1,27 +1,27 @@ - [binaries] --abyss:$CONDA/bin/ABYSS --abyss-pe:$CONDA/bin/abyss-pe --bcftools:$CONDA/bin/bcftools --bedtools:$CONDA/bin/bedtools --bwa:$CONDA/bin/bwa --gblocks:$CONDA/bin/Gblocks --lastz:$CONDA/bin/lastz --mafft:$CONDA/bin/mafft --muscle:$CONDA/bin/muscle --pilon:$CONDA/bin/pilon --raxml-ng:$CONDA/bin/raxml-ng --samtools:$CONDA/bin/samtools --seqtk:$CONDA/bin/seqtk --spades:$CONDA/bin/spades.py --trimal:$CONDA/bin/trimal --velvetg:$CONDA/bin/velvetg --velveth:$CONDA/bin/velveth --snakemake:$CONDA/bin/Snakemake -+abyss:$EBROOTABYSS/bin/ABYSS -+abyss-pe:$EBROOTABYSS/bin/abyss-pe -+bcftools:$EBROOTBCFTOOLS/bin/bcftools -+bedtools:$EBROOTBEDTOOLS/bin/bedtools -+bwa:$EBROOTBWA/bin/bwa -+gblocks:$EBROOTGBLOCKS/Gblocks -+lastz:$EBROOTLASTZ/bin/lastz -+mafft:$EBROOTMAFFT/bin/mafft -+muscle:$EBROOTMUSCLE/bin/muscle -+pilon:$EBROOTPILON/bin/pilon -+raxml-ng:$EBROOTRAXMLMINNG/bin/raxml-ng -+samtools:$EBROOTSAMTOOLS/bin/samtools -+seqtk:$EBROOTSEQTK/bin/seqtk -+spades:$EBROOTSPADES/bin/spades.py -+trimal:$EBROOTTRIMAL/bin/trimal -+velvetg:$EBROOTVELVET/bin/velvetg -+velveth:$EBROOTVELVET/bin/velveth -+snakemake:$EBROOTSNAKEMAKE/bin/snakemake - - [workflows] --mapping:$WORKFLOWS/mapping/Snakefile --correction:$WORKFLOWS/contig-correction/Snakefile --phasing:$WORKFLOWS/phasing/Snakefile -+mapping:$EBROOTPHYLUCE/phyluce/workflows/mapping/Snakefile -+correction:$EBROOTPHYLUCE/phyluce/workflows/contig-correction/Snakefile -+phasing:$EBROOTPHYLUCE/phyluce/workflows/phasing/Snakefile - - #---------------- - # Advanced diff --git a/271_phyluce/phyluce-1.7.3_removal-Bio-Alphabet.patch b/271_phyluce/phyluce-1.7.3_removal-Bio-Alphabet.patch deleted file mode 100644 index 82e9c87c..00000000 --- a/271_phyluce/phyluce-1.7.3_removal-Bio-Alphabet.patch +++ /dev/null @@ -1,21 +0,0 @@ -# removal of the Bio.Alphabet - it is not part of Biopython anymore (since v1.78) -# https://biopython.org/wiki/Alphabet ---- bin/ncbi/phyluce_ncbi_prep_uce_align_files_for_ncbi.orig 2024-02-01 15:53:37.732931000 +0100 -+++ bin/ncbi/phyluce_ncbi_prep_uce_align_files_for_ncbi 2024-02-01 16:16:42.885167000 +0100 -@@ -18,7 +18,6 @@ - from Bio import AlignIO - from Bio.Seq import Seq - from Bio.SeqRecord import SeqRecord --from Bio.Alphabet import IUPAC - - from phyluce import ncbi - from phyluce.log import setup_logging -@@ -127,7 +126,7 @@ - .upper() - ) - new_record = SeqRecord( -- Seq(new_seq, IUPAC.IUPACAmbiguousDNA()), -+ Seq(new_seq), - id=new_id, - name="", - description="", diff --git a/271_phyluce/phyluce.conf b/271_phyluce/phyluce.conf deleted file mode 100644 index 6bb17510..00000000 --- a/271_phyluce/phyluce.conf +++ /dev/null @@ -1,38 +0,0 @@ -[binaries] -abyss:$EBROOTABYSS/bin/ABYSS -abyss-pe:$EBROOTABYSS/bin/abyss-pe -bcftools:$EBROOTBCFTOOLS/bin/bcftools -bedtools:$EBROOTBEDTOOLS/bin/bedtools -bwa:$EBROOTBWA/bin/bwa -gblocks:$EBROOTGBLOCKS/Gblocks -lastz:$EBROOTLASTZ/bin/lastz -mafft:$EBROOTMAFFT/bin/mafft -muscle:$EBROOTMUSCLE/bin/muscle -pilon:java -Xmx8G -jar $EBROOTPILON/pilon.jar -raxml-ng:$EBROOTRAXMLMINNG/bin/raxml-ng -samtools:$EBROOTSAMTOOLS/bin/samtools -seqtk:$EBROOTSEQTK/bin/seqtk -spades:$EBROOTSPADES/bin/spades.py -trimal:$EBROOTTRIMAL/bin/trimal -velvetg:$EBROOTVELVET/bin/velvetg -velveth:$EBROOTVELVET/bin/velveth -snakemake:$EBROOTSNAKEMAKE/bin/snakemake - -[workflows] -mapping:$EBROOTPHYLUCE/phyluce/workflows/mapping/Snakefile -correction:$EBROOTPHYLUCE/phyluce/workflows/contig-correction/Snakefile -phasing:$EBROOTPHYLUCE/phyluce/workflows/phasing/Snakefile - -#---------------- -# Advanced -#---------------- - -[headers] -trinity:comp\d+_c\d+_seq\d+|c\d+_g\d+_i\d+|TR\d+\|c\d+_g\d+_i\d+|TRINITY_DN\d+_c\d+_g\d+_i\d+ -velvet:node_\d+ -abyss:node_\d+ -idba:contig-\d+_\d+ -spades:NODE_\d+_length_\d+_cov_\d+.\d+ - -[spades] -cov_cutoff:5 diff --git a/271_phyluce/phyluce.conf.orig b/271_phyluce/phyluce.conf.orig deleted file mode 100644 index 49a396e5..00000000 --- a/271_phyluce/phyluce.conf.orig +++ /dev/null @@ -1,38 +0,0 @@ -[binaries] -abyss:$CONDA/bin/ABYSS -abyss-pe:$CONDA/bin/abyss-pe -bcftools:$CONDA/bin/bcftools -bedtools:$CONDA/bin/bedtools -bwa:$CONDA/bin/bwa -gblocks:$CONDA/bin/Gblocks -lastz:$CONDA/bin/lastz -mafft:$CONDA/bin/mafft -muscle:$CONDA/bin/muscle -pilon:$CONDA/bin/pilon -raxml-ng:$CONDA/bin/raxml-ng -samtools:$CONDA/bin/samtools -seqtk:$CONDA/bin/seqtk -spades:$CONDA/bin/spades.py -trimal:$CONDA/bin/trimal -velvetg:$CONDA/bin/velvetg -velveth:$CONDA/bin/velveth -snakemake:$CONDA/bin/Snakemake - -[workflows] -mapping:$WORKFLOWS/mapping/Snakefile -correction:$WORKFLOWS/contig-correction/Snakefile -phasing:$WORKFLOWS/phasing/Snakefile - -#---------------- -# Advanced -#---------------- - -[headers] -trinity:comp\d+_c\d+_seq\d+|c\d+_g\d+_i\d+|TR\d+\|c\d+_g\d+_i\d+|TRINITY_DN\d+_c\d+_g\d+_i\d+ -velvet:node_\d+ -abyss:node_\d+ -idba:contig-\d+_\d+ -spades:NODE_\d+_length_\d+_cov_\d+.\d+ - -[spades] -cov_cutoff:5 diff --git a/271_phyluce/phyluce_ncbi_prep_uce_align_files_for_ncbi b/271_phyluce/phyluce_ncbi_prep_uce_align_files_for_ncbi deleted file mode 100644 index 4001fa3d..00000000 --- a/271_phyluce/phyluce_ncbi_prep_uce_align_files_for_ncbi +++ /dev/null @@ -1,142 +0,0 @@ -#!/usr/bin/env python -# -*- coding: utf-8 -*- - -""" -(c) 2014 Brant Faircloth || http://faircloth-lab.org/ -All rights reserved. - -This code is distributed under a 3-clause BSD license. Please see -LICENSE.txt for more information. - -Created on 09 June 2014 15:00 PDT (-0700) -""" - -import os -import argparse -import configparser - -from Bio import AlignIO -from Bio.Seq import Seq -from Bio.SeqRecord import SeqRecord - -from phyluce import ncbi -from phyluce.log import setup_logging -from phyluce.helpers import ( - is_dir, - is_file, - get_alignment_files, - get_file_extensions, - FullPaths, -) - - -import pdb - - -def get_args(): - """Get arguments from CLI""" - parser = argparse.ArgumentParser( - description="""Format a monolithic NCBI fasta file for tbl2asn from alignments""" - ) - parser.add_argument( - "--alignments", - required=True, - type=is_dir, - help="""The directory containing alignments""", - ) - parser.add_argument( - "--conf", required=True, type=is_file, help="""The config file name""" - ) - parser.add_argument( - "--output", required=True, help="""The output file name""" - ) - parser.add_argument( - "--input-format", - dest="input_format", - choices=[ - "fasta", - "nexus", - "phylip", - "phylip-relaxed", - "clustal", - "emboss", - "stockholm", - ], - default="nexus", - help="""The input alignment format""", - ) - parser.add_argument( - "--verbosity", - type=str, - choices=["INFO", "WARN", "CRITICAL"], - default="INFO", - help="""The logging level to use.""", - ) - parser.add_argument( - "--log-path", - action=FullPaths, - type=is_dir, - default=None, - help="""The path to a directory to hold logs.""", - ) - return parser.parse_args() - - -def main(): - args = get_args() - # setup logging - log, my_name = setup_logging(args) - conf = configparser.ConfigParser(allow_no_value=True) - conf.read(args.conf) - # get remapped names - remap = ncbi.get_remaps(conf) - # get alignments - alignments = get_alignment_files(log, args.alignments, args.input_format) - # get metadata from conf file - metadata = ncbi.get_metadata(conf) - vouchers = ncbi.get_vouchers(conf) - # get our excludes - taxon_excludes = ncbi.get_excludes(conf, "exclude taxa") - locus_excludes = ncbi.get_excludes(conf, "exclude loci") - log.warn("Excluding samples: {}".format(", ".join(taxon_excludes))) - log.warn("Excluding loci: {}".format(",".join(locus_excludes))) - # setup counter for unique ID - counter = 0 - log.info("Parsing alignments") - with open(args.output, "w") as outf: - for f in alignments: - uce = os.path.splitext(os.path.basename(f))[0] - if uce not in locus_excludes: - for seq in AlignIO.read(f, args.input_format): - # get species name - sp, species, partial, oldname = ncbi.get_species_name( - seq.id, remap - ) - # skip taxa in exclude list - if species in taxon_excludes or oldname in taxon_excludes: - pass - else: - new_id = ncbi.get_new_identifier( - species, uce, partial, counter, metadata, vouchers - ) - new_seq = ( - str(seq.seq) - .replace("-", "") - .replace("?", "") - .upper() - ) - new_record = SeqRecord( - Seq(new_seq), - id=new_id, - name="", - description="", - ) - outf.write(new_record.format("fasta")) - counter += 1 - # end - text = " Completed {} ".format(my_name) - log.info(text.center(65, "=")) - - -if __name__ == "__main__": - main() diff --git a/271_phyluce/phyluce_ncbi_prep_uce_align_files_for_ncbi.orig b/271_phyluce/phyluce_ncbi_prep_uce_align_files_for_ncbi.orig deleted file mode 100644 index f9930169..00000000 --- a/271_phyluce/phyluce_ncbi_prep_uce_align_files_for_ncbi.orig +++ /dev/null @@ -1,143 +0,0 @@ -#!/usr/bin/env python -# -*- coding: utf-8 -*- - -""" -(c) 2014 Brant Faircloth || http://faircloth-lab.org/ -All rights reserved. - -This code is distributed under a 3-clause BSD license. Please see -LICENSE.txt for more information. - -Created on 09 June 2014 15:00 PDT (-0700) -""" - -import os -import argparse -import configparser - -from Bio import AlignIO -from Bio.Seq import Seq -from Bio.SeqRecord import SeqRecord -from Bio.Alphabet import IUPAC - -from phyluce import ncbi -from phyluce.log import setup_logging -from phyluce.helpers import ( - is_dir, - is_file, - get_alignment_files, - get_file_extensions, - FullPaths, -) - - -import pdb - - -def get_args(): - """Get arguments from CLI""" - parser = argparse.ArgumentParser( - description="""Format a monolithic NCBI fasta file for tbl2asn from alignments""" - ) - parser.add_argument( - "--alignments", - required=True, - type=is_dir, - help="""The directory containing alignments""", - ) - parser.add_argument( - "--conf", required=True, type=is_file, help="""The config file name""" - ) - parser.add_argument( - "--output", required=True, help="""The output file name""" - ) - parser.add_argument( - "--input-format", - dest="input_format", - choices=[ - "fasta", - "nexus", - "phylip", - "phylip-relaxed", - "clustal", - "emboss", - "stockholm", - ], - default="nexus", - help="""The input alignment format""", - ) - parser.add_argument( - "--verbosity", - type=str, - choices=["INFO", "WARN", "CRITICAL"], - default="INFO", - help="""The logging level to use.""", - ) - parser.add_argument( - "--log-path", - action=FullPaths, - type=is_dir, - default=None, - help="""The path to a directory to hold logs.""", - ) - return parser.parse_args() - - -def main(): - args = get_args() - # setup logging - log, my_name = setup_logging(args) - conf = configparser.ConfigParser(allow_no_value=True) - conf.read(args.conf) - # get remapped names - remap = ncbi.get_remaps(conf) - # get alignments - alignments = get_alignment_files(log, args.alignments, args.input_format) - # get metadata from conf file - metadata = ncbi.get_metadata(conf) - vouchers = ncbi.get_vouchers(conf) - # get our excludes - taxon_excludes = ncbi.get_excludes(conf, "exclude taxa") - locus_excludes = ncbi.get_excludes(conf, "exclude loci") - log.warn("Excluding samples: {}".format(", ".join(taxon_excludes))) - log.warn("Excluding loci: {}".format(",".join(locus_excludes))) - # setup counter for unique ID - counter = 0 - log.info("Parsing alignments") - with open(args.output, "w") as outf: - for f in alignments: - uce = os.path.splitext(os.path.basename(f))[0] - if uce not in locus_excludes: - for seq in AlignIO.read(f, args.input_format): - # get species name - sp, species, partial, oldname = ncbi.get_species_name( - seq.id, remap - ) - # skip taxa in exclude list - if species in taxon_excludes or oldname in taxon_excludes: - pass - else: - new_id = ncbi.get_new_identifier( - species, uce, partial, counter, metadata, vouchers - ) - new_seq = ( - str(seq.seq) - .replace("-", "") - .replace("?", "") - .upper() - ) - new_record = SeqRecord( - Seq(new_seq, IUPAC.IUPACAmbiguousDNA()), - id=new_id, - name="", - description="", - ) - outf.write(new_record.format("fasta")) - counter += 1 - # end - text = " Completed {} ".format(my_name) - log.info(text.center(65, "=")) - - -if __name__ == "__main__": - main() diff --git a/271_phyluce/seqtk-1.4-GCC-12.3.0.eb b/271_phyluce/seqtk-1.4-GCC-12.3.0.eb deleted file mode 100644 index d19790ad..00000000 --- a/271_phyluce/seqtk-1.4-GCC-12.3.0.eb +++ /dev/null @@ -1,36 +0,0 @@ -## -# created by Thomas Eylenbosch -# updated by Pavel Tománek (INUITS) -## - -easyblock = 'ConfigureMake' - -name = 'seqtk' -version = '1.4' - -homepage = 'https://github.com/lh3/seqtk/' -description = """Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. - It seamlessly parses both FASTA and FASTQ files which can also be optionally compressed by gzip.""" - -toolchain = {'name': 'GCC', 'version': '12.3.0'} - -github_account = 'lh3' -source_urls = [GITHUB_SOURCE] -sources = ['v%(version)s.tar.gz'] -checksums = ['d124604ec24f29ed14ce127426ab90e0f3a2c0280c80d1a3ff8b1c09feede19c'] - -dependencies = [('zlib', '1.2.13')] - -skipsteps = ['configure'] - -buildopts = 'CC="$CC" CFLAGS="$CLFAGS"' - -preinstallopts = "mkdir %(installdir)s/bin && " -installopts = 'BINDIR=%(installdir)s/bin/' - -sanity_check_paths = { - 'files': ['bin/seqtk'], - 'dirs': [], -} - -moduleclass = 'bio' diff --git a/271_phyluce/trimAl-1.4.1-GCCcore-12.3.0.eb b/271_phyluce/trimAl-1.4.1-GCCcore-12.3.0.eb deleted file mode 100644 index ab4fbb5d..00000000 --- a/271_phyluce/trimAl-1.4.1-GCCcore-12.3.0.eb +++ /dev/null @@ -1,39 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Updated by: -# R.QIAO -# DeepThought, Flinders University -# and -# Pavel Tománek (INUITS) - -easyblock = 'MakeCp' - -name = 'trimAl' -version = '1.4.1' - -homepage = 'https://github.com/scapella/trimal' -description = """EVB, FEP and LIE simulator.""" - -toolchain = {'name': 'GCCcore', 'version': '12.3.0'} -toolchainopts = {'pic': True} - -github_account = 'scapella' -source_urls = [GITHUB_LOWER_SOURCE] -sources = ['v%(version)s.tar.gz'] -checksums = ['cb8110ca24433f85c33797b930fa10fe833fa677825103d6e7f81dd7551b9b4e'] - -builddependencies = [ - ('binutils', '2.40'), - -] -start_dir = 'source' - -files_to_copy = [(['trimal', 'readal', 'statal'], 'bin')] - -sanity_check_paths = { - 'files': ['bin/trimal', 'bin/readal', 'bin/statal'], - 'dirs': [] -} - -sanity_check_commands = ["trimal -h"] - -moduleclass = 'bio' diff --git a/271_phyluce/unused_econfigs/Cbc-2.10.11-foss-2023a.eb b/271_phyluce/unused_econfigs/Cbc-2.10.11-foss-2023a.eb deleted file mode 100644 index 9aac2887..00000000 --- a/271_phyluce/unused_econfigs/Cbc-2.10.11-foss-2023a.eb +++ /dev/null @@ -1,64 +0,0 @@ -easyblock = "ConfigureMake" - -name = 'Cbc' -version = '2.10.11' - -homepage = "https://github.com/coin-or/Cbc" -description = """Cbc (Coin-or branch and cut) is an open-source mixed integer linear programming -solver written in C++. It can be used as a callable library or using a -stand-alone executable.""" - -toolchain = {'name': 'foss', 'version': '2023a'} -toolchainopts = {'pic': True, 'usempi': True} - -source_urls = ['https://github.com/coin-or/Cbc/archive/refs/tags/releases/'] -sources = ['%(version)s.tar.gz'] -checksums = ['1fb591dd88336fdaf096b8e42e46111e41671a5eb85d4ee36e45baff1678bd33'] - -builddependencies = [ - ('Autotools', '20220317'), - ('Doxygen', '1.9.7'), -# ('pkg-config', '0.29.2'),#NO! # pkgconf should be used in preference to pkg-config - ('pkgconf', '1.9.5'), -] - -dependencies = [ - ('METIS', '5.1.0'), - ('MUMPS', '5.6.1', '-metis'), - ('CoinUtils', '2.11.10'),#done - ('Osi', '0.108.9'),#done - ('Clp', '1.17.9'),#done - ('Cgl', '0.60.8'),#done - ('bzip2', '1.0.8'), - ('zlib', '1.2.13'), -] - -# Use BLAS/LAPACK from OpenBLAS -configopts = '--with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK" ' -# Use METIS AND MUMPS from EB -configopts += '--with-metis-lib="-lmetis" ' -configopts += '--with-mumps-lib="-lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord" ' -# Disable GLPK, dependencies have to be built with it as well -configopts += '--without-glpk ' -# Use CoinUtils from EB -configopts += '--with-coinutils-lib="-lCoinUtils" ' -configopts += '--with-coinutils-datadir=$EBROOTCOINUTILS/share/coin/Data' -# Use Clp from EB -configopts += '--with-clp-lib="-lOsiClp -lClpSolver -lClp" ' -configopts += '--with-clp-datadir=$EBROOTCLP/share/coin/Data ' -# Use Osi from EB (also needs links to Clp due to OsiClpSolver) -configopts += '--with-osi-lib="-lOsiClp -lClpSolver -lClp -lOsi" ' -configopts += '--with-osi-datadir=$EBROOTOSI/share/coin/Data ' -# Use Cgl from EB -configopts += '--with-cgl-lib="-lCgl" ' -configopts += '--with-cgl-datadir=$EBROOTCGL/share/coin/Data ' - -sanity_check_paths = { - 'files': ['bin/cbc'] + ['lib/lib%s.%s' % (x, SHLIB_EXT) for x in ['Cbc', 'CbcSolver', 'OsiCbc']], - 'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'] -} - -# other coin-or projects expect instead of -modextrapaths = {'CPATH': 'include/coin'} - -moduleclass = "math" diff --git a/271_phyluce/unused_econfigs/Cgl-0.60.8-foss-2023a.eb b/271_phyluce/unused_econfigs/Cgl-0.60.8-foss-2023a.eb deleted file mode 100644 index 0925896e..00000000 --- a/271_phyluce/unused_econfigs/Cgl-0.60.8-foss-2023a.eb +++ /dev/null @@ -1,51 +0,0 @@ -easyblock = "ConfigureMake" - -name = 'Cgl' -version = '0.60.8' - -homepage = "https://github.com/coin-or/Cgl" -description = """The COIN-OR Cut Generation Library (Cgl) is a collection of cut generators that -can be used with other COIN-OR packages that make use of cuts, such as, among -others, the linear solver Clp or the mixed integer linear programming solvers -Cbc or BCP. Cgl uses the abstract class OsiSolverInterface (see Osi) to use or -communicate with a solver. It does not directly call a solver.""" - -toolchain = {'name': 'foss', 'version': '2023a'} -toolchainopts = {'pic': True, 'usempi': True} - -source_urls = ['https://github.com/coin-or/Cgl/archive/refs/tags/releases/'] -sources = ['%(version)s.tar.gz'] -checksums = ['1482ba38afb783d124df8d5392337f79fdd507716e9f1fb6b98fc090acd1ad96'] - -builddependencies = [ - ('Autotools', '20220317'), - ('Doxygen', '1.9.7'), - # ('pkg-config', '0.29.2'), # pkgconf should be used in preference to pkg-config - ('pkgconf', '1.9.5'), -] - -dependencies = [ - ('CoinUtils', '2.11.10'), - ('Osi', '0.108.9'), - ('Clp', '1.17.9'), -] - -# Use CoinUtils from EB -configopts = '--with-coinutils-lib="-lCoinUtils" ' -configopts += '--with-coinutils-datadir=$EBROOTCOINUTILS/share/coin/Data' -# Use Clp from EB -configopts += '--with-clp-lib="-lOsiClp -lClpSolver -lClp" ' -configopts += '--with-clp-datadir=$EBROOTCLP/share/coin/Data ' -# Use Osi from EB (also needs links to Clp due to OsiClpSolver) -configopts += '--with-osi-lib="-lOsiClp -lClpSolver -lClp -lOsi" ' -configopts += '--with-osi-datadir=$EBROOTOSI/share/coin/Data ' - -sanity_check_paths = { - 'files': ['lib/libCgl.%s' % SHLIB_EXT], - 'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'] -} - -# other coin-or projects expect instead of -modextrapaths = {'CPATH': 'include/coin'} - -moduleclass = "math" diff --git a/271_phyluce/unused_econfigs/Clp-1.17.9-foss-2023a.eb b/271_phyluce/unused_econfigs/Clp-1.17.9-foss-2023a.eb deleted file mode 100644 index 8b4fedf4..00000000 --- a/271_phyluce/unused_econfigs/Clp-1.17.9-foss-2023a.eb +++ /dev/null @@ -1,61 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Clp' -version = '1.17.9' - -homepage = "https://github.com/coin-or/Clp" -description = """Clp (Coin-or linear programming) is an open-source linear programming solver. -It is primarily meant to be used as a callable library, but a basic, -stand-alone executable version is also available.""" - -toolchain = {'name': 'foss', 'version': '2023a'} -toolchainopts = {'pic': True, 'usempi': True} - -source_urls = ['https://github.com/coin-or/Clp/archive/refs/tags/releases/'] -sources = ['%(version)s.tar.gz'] -checksums = ['b02109be54e2c9c6babc9480c242b2c3c7499368cfca8c0430f74782a694a49f'] - -builddependencies = [ - ('Autotools', '20220317'), - ('Doxygen', '1.9.7'), - ('pkgconf', '1.9.5'), -] - -dependencies = [ - ('METIS', '5.1.0'), - ('MUMPS', '5.6.1', '-metis'), - ('CoinUtils', '2.11.10'), - ('Osi', '0.108.9'), - ('bzip2', '1.0.8'), - ('zlib', '1.2.13'), -] - -# Use BLAS/LAPACK from OpenBLAS -configopts = '--with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK" ' - -# Use METIS AND MUMPS from EB -# --with-metis-lib is ignored -configopts += '--with-metis-lib="-lmetis" ' -configopts += '--with-mumps-lib="-lesmumps -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord -lmpi_mpifh ' -configopts += '-lmetis -lscotch -lptscotch -lptscotcherr -lscotcherrexit -lscotcherr -lscalapack" ' - -# Disable GLPK because Clp requires headers from its sources -configopts += '--without-glpk ' - -# Use CoinUtils from EB -configopts += '--with-coinutils-lib="-lCoinUtils" ' -configopts += '--with-coinutils-datadir=$EBROOTCOINUTILS/share/coin/Data' - -# Use Osi from EB -configopts += '--with-osi-lib="-lOsi" ' -configopts += '--with-osi-datadir=$EBROOTOSI/share/coin/Data ' - -sanity_check_paths = { - 'files': ['bin/clp'] + ['lib/lib%s.%s' % (x, SHLIB_EXT) for x in ['Clp', 'ClpSolver', 'OsiClp']], - 'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'] -} - -# other coin-or projects expect instead of -modextrapaths = {'CPATH': 'include/coin'} - -moduleclass = "math" diff --git a/271_phyluce/unused_econfigs/CoinUtils-2.11.10-GCC-12.3.0.eb b/271_phyluce/unused_econfigs/CoinUtils-2.11.10-GCC-12.3.0.eb deleted file mode 100644 index 642d353e..00000000 --- a/271_phyluce/unused_econfigs/CoinUtils-2.11.10-GCC-12.3.0.eb +++ /dev/null @@ -1,36 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'CoinUtils' -version = '2.11.10' - -homepage = "https://github.com/coin-or/CoinUtils" -description = """CoinUtils (Coin-OR Utilities) is an open-source collection of classes and -functions that are generally useful to more than one COIN-OR project.""" - -source_urls = ['https://github.com/coin-or/CoinUtils/archive/refs/tags/releases/'] -sources = ['%(version)s.tar.gz'] -checksums = ['80c7c215262df8d6bd2ba171617c5df844445871e9891ec6372df12ccbe5bcfd'] - -# NOTE: this esyconfig for CoinUtils provides a minimal build not using BLAS/LAPACK or MPI -toolchain = {'name': 'GCC', 'version': '12.3.0'} - -builddependencies = [ - ('Autotools', '20220317'), - ('Doxygen', '1.9.7'), - ('pkgconf', '1.9.5'), -] - -dependencies = [ - ('bzip2', '1.0.8'), - ('zlib', '1.2.13'), -] - -sanity_check_paths = { - 'files': ['lib/libCoinUtils.%s' % SHLIB_EXT], - 'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'] -} - -# other coin-or projects expect instead of -modextrapaths = {'CPATH': 'include/coin'} - -moduleclass = "math" diff --git a/271_phyluce/unused_econfigs/Osi-0.108.9-GCC-12.3.0.eb b/271_phyluce/unused_econfigs/Osi-0.108.9-GCC-12.3.0.eb deleted file mode 100644 index 412433c1..00000000 --- a/271_phyluce/unused_econfigs/Osi-0.108.9-GCC-12.3.0.eb +++ /dev/null @@ -1,49 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Osi' -version = '0.108.9' - -homepage = "https://github.com/coin-or/Osi" -description = """Osi (Open Solver Interface) provides an abstract base class to a generic linear -programming (LP) solver, along with derived classes for specific solvers. Many -applications may be able to use the Osi to insulate themselves from a specific -LP solver. That is, programs written to the OSI standard may be linked to any -solver with an OSI interface and should produce correct results. The OSI has -been significantly extended compared to its first incarnation. Currently, the -OSI supports linear programming solvers and has rudimentary support for integer -programming.""" - -toolchain = {'name': 'GCC', 'version': '12.3.0'} - -source_urls = ['https://github.com/coin-or/Osi/archive/refs/tags/releases/'] -sources = ['%(version)s.tar.gz'] -checksums = ['8b09802960d7d4fd9579b3e4320bfb36e7f8dca5e5094bf1f5edf1b7003f5562'] - -builddependencies = [ - ('Autotools', '20220317'), - ('Doxygen', '1.9.7'), - # ('pkg-config', '0.29.2'), # pkgconf should be used in preference to pkg-config - ('pkgconf', '1.9.5'), -] - -dependencies = [ - ('CoinUtils', '2.11.10'), - ('bzip2', '1.0.8'), - ('zlib', '1.2.13'), -] - -# Disable GLPK because Osi requires GLPK<=4.48 -configopts = '--without-glpk ' -# Use CoinUtils from EB -configopts += '--with-coinutils-lib="-lCoinUtils" --with-coinutils-incdir=$EBROOTCOINUTILS/include/coin ' -configopts += '--with-coinutils-datadir=$EBROOTCOINUTILS/share/coin/Data' - -sanity_check_paths = { - 'files': ['lib/libOsi.%s' % SHLIB_EXT, 'lib/libOsiCommonTests.%s' % SHLIB_EXT], - 'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'] -} - -# other coin-or projects expect instead of -modextrapaths = {'CPATH': 'include/coin'} - -moduleclass = "math" diff --git a/271_phyluce/unused_econfigs/PuLP-2.8.0-foss-2023a.eb b/271_phyluce/unused_econfigs/PuLP-2.8.0-foss-2023a.eb deleted file mode 100644 index 24717851..00000000 --- a/271_phyluce/unused_econfigs/PuLP-2.8.0-foss-2023a.eb +++ /dev/null @@ -1,36 +0,0 @@ -# Contribution by -# DeepThought, Flinders University -# R.QIAO -# Updated: Petr Král (INUITS), Pavel Tománek (INUITS) - -easyblock = 'PythonPackage' - -name = 'PuLP' -version = '2.8.0' - -homepage = 'https://github.com/coin-or/pulp' -description = """ -PuLP is an LP modeler written in Python. PuLP can generate MPS or LP files and -call GLPK, COIN-OR CLP/CBC, CPLEX, GUROBI, MOSEK, XPRESS, CHOCO, MIPCL, SCIP to -solve linear problems. -""" - -toolchain = {'name': 'foss', 'version': '2023a'} - -sources = [SOURCE_TAR_GZ] -checksums = ['4903bf96110bbab8ed2c68533f90565ebb76aa367d9e4df38e51bf727927c125'] - -dependencies = [ - ('Python', '3.11.3'), - ('GLPK', '5.0'), - ('Cbc', '2.10.11'), -] - -download_dep_fail = True -use_pip = True - -sanity_pip_check = True - -sanity_check_commands = ['pulptest'] - -moduleclass = 'tools' diff --git a/271_phyluce/unused_econfigs/pkg-config-0.29.2-GCCcore-12.3.0.eb b/271_phyluce/unused_econfigs/pkg-config-0.29.2-GCCcore-12.3.0.eb deleted file mode 100644 index ac992f03..00000000 --- a/271_phyluce/unused_econfigs/pkg-config-0.29.2-GCCcore-12.3.0.eb +++ /dev/null @@ -1,36 +0,0 @@ -# # pkgconf should be used in preference to pkg-config -# # This is included for use only in software that fails to build when using pkgconf -# easyblock = 'ConfigureMake' - -# name = 'pkg-config' -# version = '0.29.2' - -# homepage = 'https://www.freedesktop.org/wiki/Software/pkg-config/' - -# description = """ -# pkg-config is a helper tool used when compiling applications and libraries. -# It helps you insert the correct compiler options on the command line so an -# application can use gcc -o test test.c `pkg-config --libs --cflags glib-2.0` -# for instance, rather than hard-coding values on where to find glib (or other -# libraries). -# """ - -# toolchain = {'name': 'GCCcore', 'version': '12.2.0'} - -# source_urls = ['https://pkg-config.freedesktop.org/releases/'] -# sources = [SOURCELOWER_TAR_GZ] -# checksums = ['6fc69c01688c9458a57eb9a1664c9aba372ccda420a02bf4429fe610e7e7d591'] - -# builddependencies = [('binutils', '2.39')] - -# # don't use PAX, it might break. -# tar_config_opts = True - -# configopts = " --with-internal-glib" - -# sanity_check_paths = { -# 'files': ['bin/pkg-config'], -# 'dirs': [], -# } - -# moduleclass = 'devel' \ No newline at end of file