BUSCO version 5.8.3 for ccrsoft/2024.04

config/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.5.0-foss-2023b.eb

@@ -0,0 +1,78 @@
+# Updated by: Pavel Grochal (INUITS)
+# License: GPLv2
+
+easyblock = 'ConfigureMake'
+
+name = 'AUGUSTUS'
+version = '3.5.0'
+
+homepage = 'https://bioinf.uni-greifswald.de/augustus/'
+description = "AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences"
+
+toolchain = {'name': 'foss', 'version': '2023b'}
+
+github_account = 'Gaius-Augustus'
+source_urls = [GITHUB_SOURCE]
+sources = ['v%(version)s.tar.gz']
+patches = ['%(name)s-3.5.0_sqliteDB_cstdint_include.patch']
+checksums = [
+    '5ed6ce6106303b800c5e91d37a250baff43b20824657b853ae04d11ad8bdd686',  # v3.5.0.tar.gz
+    '1c5e1813f100531ec8a9fd0bc948612d37a5676eb8f5d59601ed2cfed65fa255',  # AUGUSTUS-3.5.0_sqliteDB_cstdint_include.patch
+]
+
+builddependencies = [
+    ('Python', '3.11.5'),
+]
+
+dependencies = [
+    ('zlib', '1.2.13'),
+    ('Boost', '1.83.0'),
+    ('GSL', '2.7'),
+    ('SAMtools', '1.19.2'),
+    ('HTSlib', '1.19.1'),  # also provides tabix
+    ('BCFtools', '1.19'),
+    ('lpsolve', '5.5.2.11'),
+    ('SuiteSparse', '7.7.0', '-METIS-5.1.0'),
+    ('BamTools', '2.5.2'),
+    ('SQLite', '3.43.1'),
+    ('lpsolve', '5.5.2.11'),
+]
+
+skipsteps = ['configure']
+
+# run "make clean" to avoid using binaries included with the source tarball
+prebuildopts = "make clean && "
+
+_tmpl = 'INCLUDE_PATH_{dep}=-I{root}{incl} LIBRARY_PATH_{dep}="-L{root}{lib} -Wl,-rpath,{root}{lib}"'
+
+buildopts = ' '.join([
+    'COMPGENEPRED=true SQLITE=true ZIPINPUT=true MYSQL=false CXX="$CXX" ',
+    _tmpl.format(dep='ZLIB', root='$EBROOTZLIB', incl='/include', lib='/lib'),
+    _tmpl.format(dep='BOOST', root='$EBROOTBOOST', incl='/include', lib='/lib'),
+    _tmpl.format(dep='LPSOLVE', root='$EBROOTLPSOLVE', incl='/include', lib='/lib'),
+    _tmpl.format(dep='SUITESPARSE', root='$EBROOTSUITESPARSE', incl='/include', lib='/lib'),
+    _tmpl.format(dep='GSL', root='$EBROOTGSL', incl='/include', lib='/lib'),
+    _tmpl.format(dep='SQLITE', root='$EBROOTSQLITE', incl='/include', lib='/lib'),
+    _tmpl.format(dep='BAMTOOLS', root='$EBROOTBAMTOOLS', incl='/include/bamtools', lib='/lib'),
+    _tmpl.format(dep='HTSLIB', root='$EBROOTHTSLIB', incl='/include/htslib', lib='/lib'),
+])
+
+preinstallopts = "sed -i '/ln -sf/d' Makefile && "
+installopts = 'INSTALLDIR=%(installdir)s '
+
+sanity_check_paths = {
+    'files': ['bin/augustus', 'bin/bam2hints', 'bin/etraining', 'bin/fastBlockSearch',
+              'bin/filterBam', 'bin/getSeq', 'bin/homGeneMapping', 'bin/joingenes',
+              'bin/load2sqlitedb', 'bin/prepareAlign'],
+    'dirs': ['config', 'scripts'],
+}
+sanity_check_commands = ['augustus --help']
+
+modextrapaths = {'PATH': 'scripts'}
+modextravars = {
+    'AUGUSTUS_BIN_PATH': '%(installdir)s/bin',
+    'AUGUSTUS_CONFIG_PATH': '%(installdir)s/config',
+    'AUGUSTUS_SCRIPTS_PATH': '%(installdir)s/scripts',
+}
+
+moduleclass = 'bio'

config/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.5.0_sqliteDB_cstdint_include.patch

@@ -0,0 +1,43 @@
+From 1ed97dc4ce2909c5f89737005b8ea4a664fbe728 Mon Sep 17 00:00:00 2001
+From: Kuoi <kuoi@bioarchlinux.org>
+Date: Sun, 11 Jun 2023 23:47:49 +0800
+Subject: [PATCH] fix: gcc13 failed with this
+
+---
+ include/sqliteDB.hh | 1 +
+ 1 file changed, 1 insertion(+)
+
+diff --git a/include/sqliteDB.hh b/include/sqliteDB.hh
+index e66374b9d..67a37826f 100644
+--- a/include/sqliteDB.hh
++++ b/include/sqliteDB.hh
+@@ -11,6 +11,7 @@
+ #include <string>
+ #include <vector>
+ #include <sqlite3.h>
++#include <cstdint>
+
+ using namespace std;
+
+From 3dbe752e4cf3f6778168166a2c662d02d8623f15 Mon Sep 17 00:00:00 2001
+From: Kuoi <kuoi@bioarchlinux.org>
+Date: Mon, 12 Jun 2023 01:32:02 +0800
+Subject: [PATCH] fix: without it compile fail
+
+---
+ auxprogs/homGeneMapping/include/sqliteDB.hh | 1 +
+ 1 file changed, 1 insertion(+)
+
+diff --git a/auxprogs/homGeneMapping/include/sqliteDB.hh b/auxprogs/homGeneMapping/include/sqliteDB.hh
+index e842bcf9d..67338bef4 100644
+--- a/auxprogs/homGeneMapping/include/sqliteDB.hh
++++ b/auxprogs/homGeneMapping/include/sqliteDB.hh
+@@ -13,6 +13,7 @@
+ #include <string>
+ #include <vector>
+ #include <sqlite3.h>
++#include <cstdint>
+
+ using namespace std;
+
+

config/easybuild/easyconfigs/b/BUSCO/BUSCO-5.8.3-foss-2023b.eb

@@ -0,0 +1,57 @@
+# Updated by: Pavel Grochal (INUITS)
+# Updated by: Sebastien Moretti (SIB)
+
+easyblock = 'PythonPackage'
+
+name = 'BUSCO'
+version = '5.8.3'
+
+homepage = 'https://busco.ezlab.org/'
+description = "BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs"
+# software_license = 'LicenseMIT'
+
+toolchain = {'name': 'foss', 'version': '2023b'}
+
+source_urls = ['https://gitlab.com/ezlab/%(namelower)s/-/archive/%(version)s']
+sources = [SOURCELOWER_TAR_BZ2]
+checksums = ['b1a46c93b636ca59fd7529f8fba28774d9998c9a03d3f1fa8776a1fb08aa8b3f']
+
+dependencies = [
+    ('Python', '3.11.5'),
+    ('SciPy-bundle', '2023.11'),  # for pandas
+    ('R', '4.4.1'),  # for R and ggplot2
+    ('Biopython', '1.84'),
+    ('BLAST+', '2.14.1'),
+    ('HMMER', '3.4'),
+    ('prodigal', '2.6.3'),
+    ('AUGUSTUS', '3.5.0'),
+    ('SEPP', '4.5.5'),
+    ('MetaEuk', '7'),
+    ('BBMap', '39.01'),
+    ('miniprot', '0.14'),
+]
+
+use_pip = True
+download_dep_fail = True
+sanity_pip_check = True
+
+postinstallcmds = [
+    'mkdir -p %(installdir)s/bin %(installdir)s/doc',
+    'cp %(builddir)s/%(namelower)s-%(version)s/scripts/* %(installdir)s/bin',
+    'cp %(builddir)s/%(namelower)s-%(version)s/LICENSE %(installdir)s/doc',
+    'cp -r %(builddir)s/%(namelower)s-%(version)s/test_data %(installdir)s',
+    'cp -r %(builddir)s/%(namelower)s-%(version)s/config %(installdir)s',
+]
+
+sanity_check_paths = {
+    'files': ['bin/busco', 'bin/generate_plot.py'],
+    'dirs': ['test_data', 'lib/python%(pyshortver)s/site-packages/busco']
+}
+
+sanity_check_commands = [
+    "busco --help",
+    "busco -i %(installdir)s/test_data/bacteria/genome.fna --cpu %(parallel)s  --mode geno --out test_bacteria.out",
+    "busco -i %(installdir)s/test_data/eukaryota/genome.fna --cpu %(parallel)s --mode geno --out test_eukaryota.out",
+]
+
+moduleclass = 'bio'

config/easybuild/easyconfigs/m/MetaEuk/MetaEuk-7-GCC-13.2.0.eb

@@ -0,0 +1,31 @@
+easyblock = 'CMakeMake'
+
+name = 'MetaEuk'
+version = '7'
+local_commit = 'bba0d80'
+
+homepage = 'https://metaeuk.soedinglab.org'
+description = """MetaEuk is a modular toolkit designed for large-scale gene discovery and annotation in eukaryotic
+ metagenomic contigs."""
+
+toolchain = {'name': 'GCC', 'version': '13.2.0'}
+
+source_urls = ['https://github.com/soedinglab/%(namelower)s/archive']
+sources = ['%%(version)s-%s.tar.gz' % local_commit]
+checksums = ['45eff3cb8e15626b1142d4717bf43a6e7a1308bc8a6eb1718c70d33d613898fa']
+
+builddependencies = [('CMake', '3.27.6')]
+
+dependencies = [
+    ('bzip2', '1.0.8'),
+    ('zlib', '1.2.13'),
+]
+
+sanity_check_paths = {
+    'files': ['bin/metaeuk'],
+    'dirs': [],
+}
+
+sanity_check_commands = ["metaeuk --help"]
+
+moduleclass = 'bio'

config/easybuild/easyconfigs/s/SEPP/SEPP-4.5.5-foss-2023b.eb

@@ -0,0 +1,45 @@
+# Author: Pavel Grochal (INUITS)
+# License: GPLv2
+# Updated to v4.5.1 by:
+# R.QIAO <rob.qiao@flinders.edu.au>
+# DeepThought, Flinders University
+
+name = 'SEPP'
+version = '4.5.5'
+
+homepage = 'https://github.com/smirarab/sepp'
+description = """SATe-enabled Phylogenetic Placement - addresses the problem of phylogenetic
+placement of short reads into reference alignments and trees."""
+
+toolchain = {'name': 'foss', 'version': '2023b'}
+
+# https://github.com/smirarab/sepp
+github_account = 'smirarab'
+source_urls = [GITHUB_LOWER_SOURCE]
+sources = ['v%(version)s.tar.gz']
+checksums = [
+    {'v4.5.5.tar.gz': 'af6b985bc16c96cd7c57bf78b3decce448f976aea612b3fad07b91697e4e1cfd'},
+
+]
+
+dependencies = [
+    ('Python', '3.11.5'),
+    ('DendroPy', '4.6.1'),
+]
+
+fix_python_shebang_for = ['bin/*.py']
+
+use_pip = True
+download_dep_fail = True
+sanity_pip_check = True
+
+local_bin_files = ['run_sepp.py', 'run_upp.py', 'split_sequences.py']
+
+sanity_check_paths = {
+    'files': ['bin/%s' % f for f in local_bin_files],
+    'dirs': ['lib/python%(pyshortver)s/site-packages/sepp']
+}
+
+sanity_check_commands = ["%s --help" % f for f in local_bin_files]
+
+moduleclass = 'bio'

config/easybuild/easystacks/ccrsoft-2024.04-2023b-x86_64.yml

@@ -24,3 +24,61 @@ easyconfigs:
   - code-server-4.90.2.eb
   - Julia-1.10.4-linux-x86_64.eb
   - scikit-learn-1.4.0-gfbf-2023b.eb
+  - BBMap-39.01-GCC-12.2.0.eb:
+      options:
+        try-toolchain-version: '13.2.0'
+        experimental:
+        try-update-deps:
+        copy-ec:
+  - BBMap-39.01-GCC-13.2.0.eb:
+  - BLAST+-2.14.1-gompi-2023a.eb:
+      options:
+        try-toolchain-version: '2023b'
+        experimental:
+        try-update-deps:
+        copy-ec:
+  - BLAST+-2.14.1-gompi-2023b.eb:
+  - BamTools-2.5.2-GCC-12.3.0.eb:
+      options:
+        try-toolchain-version: '13.2.0'
+        experimental:
+        try-update-deps:
+        copy-ec:
+  - BamTools-2.5.2-GCC-13.2.0.eb:
+  - DendroPy-4.6.1-GCCcore-12.3.0.eb:
+      options:
+        try-toolchain-version: '13.2.0'
+        experimental:
+        try-update-deps:
+        copy-ec:
+  - DendroPy-4.6.1-GCCcore-13.2.0.eb:
+  - lpsolve-5.5.2.11-GCC-12.2.0.eb:
+      options:
+        try-toolchain-version: '13.2.0'
+        experimental:
+        try-update-deps:
+        copy-ec:
+  - lpsolve-5.5.2.11-GCC-13.2.0.eb:
+  - AUGUSTUS-3.5.0-foss-2023b.eb:
+  - MetaEuk-7-GCC-13.2.0.eb:
+  - miniprot-0.13-GCCcore-12.3.0.eb:
+      options:
+        try-toolchain-version: '13.2.0'
+        try-software-version: '0.14'
+        experimental:
+        try-update-deps:
+        copy-ec:
+  - miniprot-0.14-GCCcore-13.2.0.eb:
+      options:
+        inject-checksums: 'sha256'
+  - miniprot-0.14-GCCcore-13.2.0.eb:
+  - prodigal-2.6.3-GCCcore-12.3.0.eb:
+      options:
+        try-toolchain-version: '13.2.0'
+        experimental:
+        try-update-deps:
+        copy-ec:
+  - prodigal-2.6.3-GCCcore-13.2.0.eb:
+  - SEPP-4.5.5-foss-2023b.eb:
+  - BUSCO-5.8.3-foss-2023b.eb:
+