BUSCO for ccrsoft/2024.04 dependency easyconfigs

config/easybuild/easyconfigs/b/BBMap/BBMap-39.01-GCC-13.2.0.eb

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+easyblock = 'MakeCp'
+
+name = 'BBMap'
+version = '39.01'
+
+homepage = 'https://sourceforge.net/projects/bbmap/'
+description = "BBMap short read aligner, and other bioinformatic tools."
+
+toolchain = {'name': 'GCC', 'version': '13.2.0'}
+
+source_urls = [SOURCEFORGE_SOURCE]
+sources = ['%(name)s_%(version)s.tar.gz']
+checksums = ['98608da50130c47f3abd095b889cc87f60beeb8b96169b664bc9d849abe093e6']
+
+dependencies = [
+    ('Java', '21.0.2', '', SYSTEM),
+]
+
+prebuildopts = "cd jni && "
+buildopts = "-f makefile.linux"
+
+modloadmsg = """For improved speed, add 'usejni=t' to the command line of %(name)s tools which support the use of the compiled jni C code.
+"""
+files_to_copy = ['*']
+
+sanity_check_paths = {
+    'files': ['%(namelower)s.sh', 'jni/libbbtoolsjni.so'],
+    'dirs': [],
+}
+
+modextrapaths = {'PATH': ''}
+
+moduleclass = 'bio'

config/easybuild/easyconfigs/b/BLAST+/BLAST+-2.14.1-gompi-2023b.eb

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+# #
+# 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 = '2.14.1'
+
+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 = ['712c2dbdf0fb13cc1c2d4f4ef5dd1ce4b06c3b57e96dfea8f23e6e99f5b1650e']
+
+builddependencies = [
+    ('cpio', '2.15'),
+]
+dependencies = [
+    ('zlib', '1.2.13'),
+    ('bzip2', '1.0.8'),
+    ('PCRE', '8.45'),
+    ('Boost', '1.83.0'),
+    ('GMP', '6.3.0'),
+    ('libpng', '1.6.40'),
+    ('libjpeg-turbo', '3.0.1'),
+    ('LMDB', '0.9.31'),
+]
+
+# remove line that prepends system paths to $PATH from configure script
+preconfigopts = 'sed -i "s|^PATH=\\(.*\\)$|#PATH=\\1 |" %(start_dir)s/src/build-system/configure && '
+configopts = "--with-z=$EBROOTZLIB --with-bz2=$EBROOTBZIP2 --with-pcre=$EBROOTPCRE --with-boost=$EBROOTBOOST --with-gmp=$EBROOTGMP --with-png=$EBROOTLIBPNG --with-jpeg=$EBROOTLIBJPEGMINTURBO --with-lmdb=$EBROOTLMDB"
+
+
+sanity_check_paths = {
+    'files': ['bin/blastn', 'bin/blastp', 'bin/blastx'],
+    'dirs': [],
+}
+
+moduleclass = 'bio'

config/easybuild/easyconfigs/b/BamTools/BamTools-2.5.2-GCC-13.2.0.eb

@@ -0,0 +1,22 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+name = 'BamTools'
+version = '2.5.2'
+
+homepage = 'https://github.com/pezmaster31/bamtools'
+description = "BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files."
+
+toolchain = {'name': 'GCC', 'version': '13.2.0'}
+toolchainopts = {'pic': True}
+
+source_urls = [GITHUB_LOWER_SOURCE]
+sources = ['v%(version)s.tar.gz']
+checksums = ['4d8b84bd07b673d0ed41031348f10ca98dd6fa6a4460f9b9668d6f1d4084dfc8']
+
+builddependencies = [
+    ('CMake', '3.27.6'),
+]
+
+# https://github.com/pezmaster31/bamtools
+github_account = 'pezmaster31'
+
+moduleclass = 'bio'

config/easybuild/easyconfigs/d/DendroPy/DendroPy-4.6.1-GCCcore-13.2.0.eb

@@ -0,0 +1,44 @@
+# #
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+#
+# Copyright:: Copyright 2013-2014 The Cyprus Institute
+# Authors::   Thekla Loizou <[email protected]>
+# License::   MIT/GPL
+# $Id$
+#
+# #
+easyblock = 'PythonPackage'
+
+name = 'DendroPy'
+version = '4.6.1'
+
+homepage = 'https://dendropy.org/'
+description = """A Python library for phylogenetics and phylogenetic computing: 
+reading, writing, simulation, processing and manipulation of phylogenetic trees 
+(phylogenies) and characters."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['26fcbe1cb5831301e8f1f2e15a0563620f0b8e29e6d409dd6a2a7c957dd64c16']
+
+builddependencies = [
+    ('binutils', '2.42'),
+]
+dependencies = [
+    ('Python', '3.11.5'),
+]
+
+fix_python_shebang_for = ['bin/*.py']
+download_dep_fail = True
+sanity_pip_check = True
+use_pip = True
+
+sanity_check_paths = {
+    'files': ['bin/sumlabels.py', 'bin/sumtrees.py'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = ['sumtrees.py --help']
+
+moduleclass = 'bio'

config/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.11-GCC-13.2.0.eb

@@ -0,0 +1,27 @@
+easyblock = 'CmdCp'
+
+name = 'lpsolve'
+version = '5.5.2.11'
+
+homepage = 'https://sourceforge.net/projects/lpsolve/'
+description = "Mixed Integer Linear Programming (MILP) solver"
+
+toolchain = {'name': 'GCC', 'version': '13.2.0'}
+
+source_urls = [SOURCEFORGE_SOURCE]
+sources = ['lp_solve_%(version)s_source.tar.gz']
+checksums = ['6d4abff5cc6aaa933ae8e6c17a226df0fc0b671c438f69715d41d09fe81f902f']
+
+start_dir = '%(name)s%(version_major)s%(version_minor)s'
+files_to_copy = [
+    (['bin/ux64/liblpsolve%(version_major)s%(version_minor)s.a', 'bin/ux64/liblpsolve%(version_major)s%(version_minor)s.so'], 'lib'),
+    (['../lp*.h'], 'include'),
+]
+cmds_map = [('.*', 'sed -i "s/^c=.*/c=\'$CC\'/g" ccc && sed -i "s/^opts=.*/opts=\'$CFLAGS\'/g" ccc && sh ccc')]
+
+sanity_check_paths = {
+    'files': ['lib/liblpsolve%(version_major)s%(version_minor)s.a', 'lib/liblpsolve%(version_major)s%(version_minor)s.so'],
+    'dirs': ['include'],
+}
+
+moduleclass = 'math'

config/easybuild/easyconfigs/m/miniprot/miniprot-0.14-GCCcore-13.2.0.eb

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+easyblock = 'MakeCp'
+
+name = 'miniprot'
+version = '0.14'
+
+homepage = 'https://github.com/lh3/miniprot'
+description = """Miniprot aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift.
+It is primarily intended for annotating protein-coding genes in a new species using known genes from other species.
+Miniprot is similar to GeneWise and Exonerate in functionality but it can map proteins to whole genomes and is much
+faster at the residue alignment step."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+
+source_urls = ['https://github.com/lh3/%(name)s/archive']
+sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}]
+checksums = ['c2b6f367c1607632400f49e80d6ace882c4d01eeef7e92c771df5529fb30232b']
+
+builddependencies = [
+    ('binutils', '2.42'),
+]
+dependencies = [
+    ('zlib', '1.2.13'),
+]
+
+files_to_copy = [
+    (['*.h', '%(name)s.1', 'test', 'tex'], 'lib'),
+    (['%(name)s'], 'bin'),
+    'README.md',
+    'LICENSE.txt',
+]
+
+sanity_check_paths = {
+    'files': ['bin/%(name)s'],
+    'dirs': ['lib'],
+}
+
+moduleclass = 'bio'

config/easybuild/easyconfigs/p/prodigal/prodigal-2.6.3-GCCcore-13.2.0.eb

@@ -0,0 +1,47 @@
+# #
+# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia
+# Homepage: https://www.adelaide.edu.au/phoenix/
+#
+# Copyright::   adelaide.edu.au/phoenix
+# Authors::	Robert Qiao <[email protected]>, Exe Escobedo <[email protected]>
+# License::	GPL-v3.0
+#
+# Updated: Pavel Grochal (INUITS)
+#
+# Notes::
+# #
+
+easyblock = 'MakeCp'
+
+name = 'prodigal'
+version = '2.6.3'
+
+homepage = 'https://github.com/hyattpd/Prodigal/'
+description = """Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm)
+   is a microbial (bacterial and archaeal) gene finding program developed
+   at Oak Ridge National Laboratory and the University of Tennessee."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+
+source_urls = ['https://github.com/hyattpd/Prodigal/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['89094ad4bff5a8a8732d899f31cec350f5a4c27bcbdd12663f87c9d1f0ec599f']
+
+builddependencies = [
+    ('binutils', '2.42'),
+]
+
+files_to_copy = [
+    (['%(name)s'], 'bin'),
+    (['*.h'], 'include'),
+    (['LICENSE'], 'license'),
+]
+
+sanity_check_paths = {
+    'files': ['bin/%(name)s'],
+    'dirs': ['include', 'license'],
+}
+
+sanity_check_commands = ['%(name)s -h']
+
+moduleclass = 'bio'