{bio}[GCC/13.3.0,foss/2024a,gompi/2024a] panaroo v1.6.0, prokka v1.15.6, PRANK v170427

[verdurin]

(created using eb --new-pr)

[github-actions]

Updated software PRANK-170427-GCC-13.3.0.eb

Diff against PRANK-251117-GCC-14.2.0.eb

easybuild/easyconfigs/p/PRANK/PRANK-251117-GCC-14.2.0.eb

diff --git a/easybuild/easyconfigs/p/PRANK/PRANK-251117-GCC-14.2.0.eb b/easybuild/easyconfigs/p/PRANK/PRANK-170427-GCC-13.3.0.eb
index 5517d5575c..b086e9e5ac 100644
--- a/easybuild/easyconfigs/p/PRANK/PRANK-251117-GCC-14.2.0.eb
+++ b/easybuild/easyconfigs/p/PRANK/PRANK-170427-GCC-13.3.0.eb
@@ -6,20 +6,18 @@
 easyblock = 'MakeCp'
 
 name = 'PRANK'
-version = '251117'
-local_commit = '94b620e'
+version = '170427'
 
-homepage = 'https://ariloytynoja.github.io/prank-msa/'
+homepage = 'http://wasabiapp.org/software/prank/'
 description = """ PRANK is a probabilistic multiple alignment program for DNA,
  codon and amino-acid sequences. PRANK is based on a novel algorithm that treats
  insertions correctly and avoids over-estimation of the number of deletion events."""
 
-toolchain = {'name': 'GCC', 'version': '14.2.0'}
+toolchain = {'name': 'GCC', 'version': '13.3.0'}
 
-github_account = 'ariloytynoja'
-source_urls = [f'http://github.com/%(github_account)s/prank-msa/raw/{local_commit}/binaries']
+source_urls = ['http://wasabiapp.org/download/prank/']
 sources = ['%(namelower)s.source.%(version)s.tgz']
-checksums = ['d8a2165b001d89506e75bb28c1a3fbdc39e32b06ceb865da2e6fffe976844c95']
+checksums = ['623eb5e9b5cb0be1f49c3bf715e5fabceb1059b21168437264bdcd5c587a8859']
 
 # PRANK uses MAFFT as external tool to construct guide tree
 dependencies = [('MAFFT', '7.526', '-with-extensions')]

Diff against PRANK-170427-GCC-12.3.0.eb

easybuild/easyconfigs/p/PRANK/PRANK-170427-GCC-12.3.0.eb

diff --git a/easybuild/easyconfigs/p/PRANK/PRANK-170427-GCC-12.3.0.eb b/easybuild/easyconfigs/p/PRANK/PRANK-170427-GCC-13.3.0.eb
index 08c0f9c06b..b086e9e5ac 100644
--- a/easybuild/easyconfigs/p/PRANK/PRANK-170427-GCC-12.3.0.eb
+++ b/easybuild/easyconfigs/p/PRANK/PRANK-170427-GCC-13.3.0.eb
@@ -13,14 +13,14 @@ description = """ PRANK is a probabilistic multiple alignment program for DNA,
  codon and amino-acid sequences. PRANK is based on a novel algorithm that treats
  insertions correctly and avoids over-estimation of the number of deletion events."""
 
-toolchain = {'name': 'GCC', 'version': '12.3.0'}
+toolchain = {'name': 'GCC', 'version': '13.3.0'}
 
 source_urls = ['http://wasabiapp.org/download/prank/']
 sources = ['%(namelower)s.source.%(version)s.tgz']
 checksums = ['623eb5e9b5cb0be1f49c3bf715e5fabceb1059b21168437264bdcd5c587a8859']
 
 # PRANK uses MAFFT as external tool to construct guide tree
-dependencies = [('MAFFT', '7.520', '-with-extensions')]
+dependencies = [('MAFFT', '7.526', '-with-extensions')]
 
 start_dir = 'src'
 

Diff against PRANK-170427-GCC-11.3.0.eb

easybuild/easyconfigs/p/PRANK/PRANK-170427-GCC-11.3.0.eb

diff --git a/easybuild/easyconfigs/p/PRANK/PRANK-170427-GCC-11.3.0.eb b/easybuild/easyconfigs/p/PRANK/PRANK-170427-GCC-13.3.0.eb
index 0da901c477..b086e9e5ac 100644
--- a/easybuild/easyconfigs/p/PRANK/PRANK-170427-GCC-11.3.0.eb
+++ b/easybuild/easyconfigs/p/PRANK/PRANK-170427-GCC-13.3.0.eb
@@ -13,14 +13,14 @@ description = """ PRANK is a probabilistic multiple alignment program for DNA,
  codon and amino-acid sequences. PRANK is based on a novel algorithm that treats
  insertions correctly and avoids over-estimation of the number of deletion events."""
 
-toolchain = {'name': 'GCC', 'version': '11.3.0'}
+toolchain = {'name': 'GCC', 'version': '13.3.0'}
 
 source_urls = ['http://wasabiapp.org/download/prank/']
 sources = ['%(namelower)s.source.%(version)s.tgz']
 checksums = ['623eb5e9b5cb0be1f49c3bf715e5fabceb1059b21168437264bdcd5c587a8859']
 
 # PRANK uses MAFFT as external tool to construct guide tree
-dependencies = [('MAFFT', '7.505', '-with-extensions')]
+dependencies = [('MAFFT', '7.526', '-with-extensions')]
 
 start_dir = 'src'
 

Updated software panaroo-1.6.0-foss-2024a.eb

Diff against panaroo-1.5.1-foss-2023a.eb

easybuild/easyconfigs/p/panaroo/panaroo-1.5.1-foss-2023a.eb

diff --git a/easybuild/easyconfigs/p/panaroo/panaroo-1.5.1-foss-2023a.eb b/easybuild/easyconfigs/p/panaroo/panaroo-1.6.0-foss-2024a.eb
index e955b1f479..659ddb1bca 100644
--- a/easybuild/easyconfigs/p/panaroo/panaroo-1.5.1-foss-2023a.eb
+++ b/easybuild/easyconfigs/p/panaroo/panaroo-1.6.0-foss-2024a.eb
@@ -3,29 +3,29 @@
 easyblock = 'PythonBundle'
 
 name = 'panaroo'
-version = '1.5.1'
+version = '1.6.0'
 
 homepage = 'https://gtonkinhill.github.io/panaroo/'
 description = "A pangenome analysis pipeline."
 
-toolchain = {'name': 'foss', 'version': '2023a'}
+toolchain = {'name': 'foss', 'version': '2024a'}
 
 dependencies = [
-    ('Python', '3.11.3'),
+    ('Python', '3.12.3'),
     ('CD-HIT', '4.8.1'),
     ('PRANK', '170427'),
-    ('Biopython', '1.83'),
-    ('SciPy-bundle', '2023.07'),
-    ('networkx', '3.1'),
-    ('edlib', '1.3.9'),
-    ('tqdm', '4.66.1'),
-    ('matplotlib', '3.7.2'),
-    ('scikit-learn', '1.3.1'),
-    ('plotly.py', '5.16.0'),
-    ('DendroPy', '4.6.1'),
-    ('pyfaidx', '0.8.1.1'),
-    ('prokka', '1.14.5'),
-    ('python-igraph', '0.11.4'),
+    ('Biopython', '1.84'),
+    ('SciPy-bundle', '2024.05'),
+    ('networkx', '3.4.2'),
+    ('edlib', '1.3.9.post1'),
+    ('tqdm', '4.66.5'),
+    ('matplotlib', '3.9.2'),
+    ('scikit-learn', '1.6.1'),
+    ('plotly.py', '5.24.1'),
+    ('DendroPy', '5.0.1'),
+    ('pyfaidx', '0.8.1.2'),
+    ('prokka', '1.15.6'),
+    ('python-igraph', '0.11.9'),
 ]
 
 exts_list = [
@@ -54,7 +54,7 @@ exts_list = [
     (name, version, {
         'source_tmpl': 'v%(version)s.tar.gz',
         'source_urls': ['https://github.com/gtonkinhill/panaroo/archive/'],
-        'checksums': ['870e09f206e5c2076aff106d19fb3e9183a56be9c9b8bca0bd0ad7a5c43030ca'],
+        'checksums': ['10376ceb676c5f5f098c6d6664f9e93285b11cf53e1a43d470b1af58e7dbbfcd'],
     }),
 ]
 

Diff against panaroo-1.3.2-foss-2021b.eb

easybuild/easyconfigs/p/panaroo/panaroo-1.3.2-foss-2021b.eb

diff --git a/easybuild/easyconfigs/p/panaroo/panaroo-1.3.2-foss-2021b.eb b/easybuild/easyconfigs/p/panaroo/panaroo-1.6.0-foss-2024a.eb
index f8d80d702a..659ddb1bca 100644
--- a/easybuild/easyconfigs/p/panaroo/panaroo-1.3.2-foss-2021b.eb
+++ b/easybuild/easyconfigs/p/panaroo/panaroo-1.6.0-foss-2024a.eb
@@ -3,29 +3,29 @@
 easyblock = 'PythonBundle'
 
 name = 'panaroo'
-version = '1.3.2'
+version = '1.6.0'
 
 homepage = 'https://gtonkinhill.github.io/panaroo/'
 description = "A pangenome analysis pipeline."
 
-toolchain = {'name': 'foss', 'version': '2021b'}
+toolchain = {'name': 'foss', 'version': '2024a'}
 
 dependencies = [
-    ('Python', '3.9.6'),
+    ('Python', '3.12.3'),
     ('CD-HIT', '4.8.1'),
     ('PRANK', '170427'),
-    ('Biopython', '1.79'),
-    ('SciPy-bundle', '2021.10'),
-    ('networkx', '2.6.3'),
-    ('edlib', '1.3.9'),
-    ('tqdm', '4.62.3'),
-    ('matplotlib', '3.4.3'),
-    ('scikit-learn', '1.0.1'),
-    ('plotly.py', '5.4.0'),
-    ('DendroPy', '4.5.2'),
-    ('pyfaidx', '0.7.0'),
-    ('prokka', '1.14.5'),
-    ('python-igraph', '0.9.8')
+    ('Biopython', '1.84'),
+    ('SciPy-bundle', '2024.05'),
+    ('networkx', '3.4.2'),
+    ('edlib', '1.3.9.post1'),
+    ('tqdm', '4.66.5'),
+    ('matplotlib', '3.9.2'),
+    ('scikit-learn', '1.6.1'),
+    ('plotly.py', '5.24.1'),
+    ('DendroPy', '5.0.1'),
+    ('pyfaidx', '0.8.1.2'),
+    ('prokka', '1.15.6'),
+    ('python-igraph', '0.11.9'),
 ]
 
 exts_list = [
@@ -35,31 +35,29 @@ exts_list = [
     ('argh', '0.27.2', {
         'checksums': ['00c9027f6f461bcf24afe599a281bbda5cbd5dee4b6705befbea293a4ca7d221'],
     }),
-    ('peewee', '3.15.4', {
-        'checksums': ['2581520c8dfbacd9d580c2719ae259f0637a9e46eda47dfc0ce01864c6366205'],
+    ('peewee', '3.17.6', {
+        'checksums': ['cea5592c6f4da1592b7cff8eaf655be6648a1f5857469e30037bf920c03fb8fb'],
     }),
     ('taxadb', '0.12.1', {
         'checksums': ['eca577cd0f4ff2f26c7d8f68d7f5a0d2f7a2f73e623139ded2493e429b23cecd'],
     }),
-    ('biocode', '0.10.0', {
+    ('biocode', '0.11.0', {
         'preinstallopts': 'sed -i "s/python-igraph/igraph/" setup.py &&',
-        'checksums': ['ab48e0ea92f52c7fe48c6c947d4d5aa43437f16cd42a804546c71ef0e5ba2265'],
+        'checksums': ['5c0df506d07e6b073b56da360bba4dad8e0b90e4ceb6f62009ae51c56a83b162'],
     }),
-    ('gffutils', '0.11.1', {
-        'checksums': ['ca7bf814d600b389bb2d5c403dd279755118cb1476c19c6f7aecb8c51a84263c'],
+    ('gffutils', '0.13', {
+        'checksums': ['b0d52f35c014cc0330fb5c4e3c6fea127c90ccf4c5384a825cdb5c8ff330d4eb'],
     }),
-    ('intbitset', '3.0.2', {
-        'checksums': ['a300b2d5a4989857ff1d0c3971624766a89a751e315aa080c07865031ae637a7'],
+    ('intbitset', '3.1.0', {
+        'checksums': ['6e83c5ba7fda2520aa8565428bbaf842deb7293d665f3cd8281cb39254d2ff71'],
     }),
     (name, version, {
         'source_tmpl': 'v%(version)s.tar.gz',
         'source_urls': ['https://github.com/gtonkinhill/panaroo/archive/'],
-        'checksums': ['290580ce094d9f790fe992c13dddd10ed6c33b389a50c434851ce2d04e0f34db'],
+        'checksums': ['10376ceb676c5f5f098c6d6664f9e93285b11cf53e1a43d470b1af58e7dbbfcd'],
     }),
 ]
 
-sanity_check_commands = [
-    "panaroo --version"
-]
+sanity_check_commands = ['%(name)s --version']
 
 moduleclass = 'bio'

Updated software prokka-1.15.6-gompi-2024a.eb

Diff against prokka-1.14.5-gompi-2023b.eb

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

diff --git a/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2023b.eb b/easybuild/easyconfigs/p/prokka/prokka-1.15.6-gompi-2024a.eb
index bd7648a541..ba7d2cc1d0 100644
--- a/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2023b.eb
+++ b/easybuild/easyconfigs/p/prokka/prokka-1.15.6-gompi-2024a.eb
@@ -8,24 +8,25 @@
 easyblock = 'Tarball'
 
 name = 'prokka'
-version = '1.14.5'
+version = '1.15.6'
 
 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'}
+toolchain = {'name': 'gompi', 'version': '2024a'}
 
 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'),
+    ('parallel', '20240722'),
     ('tbl2asn', '20230713'),
+    ('HMMER', '3.4'),
+    ('Infernal', '1.1.5'),
 ]
 
 local_bin_files = ['prokka', 'prokka-cdd_to_hmm', 'prokka-genpept_to_fasta_db', 'prokka-tigrfams_to_hmm',
@@ -36,8 +37,8 @@ local_bin_files = ['prokka', 'prokka-cdd_to_hmm', 'prokka-genpept_to_fasta_db',
 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'],
+    'files': ['bin/%s' % x for x in local_bin_files] + ['db/cm/Bacteria', 'doc/ToDoList.txt'],
+    'dirs': ['bin', 'db',  'db/cm', 'db/genus', 'db/hmm', 'db/kingdom', 'doc'],
 }
 
 sanity_check_commands = [

Diff against prokka-1.14.5-gompi-2023a.eb

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

diff --git a/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2023a.eb b/easybuild/easyconfigs/p/prokka/prokka-1.15.6-gompi-2024a.eb
index 2e84effbc5..ba7d2cc1d0 100644
--- a/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2023a.eb
+++ b/easybuild/easyconfigs/p/prokka/prokka-1.15.6-gompi-2024a.eb
@@ -8,24 +8,25 @@
 easyblock = 'Tarball'
 
 name = 'prokka'
-version = '1.14.5'
+version = '1.15.6'
 
 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': '2023a'}
+toolchain = {'name': 'gompi', 'version': '2024a'}
 
 source_urls = ['https://github.com/tseemann/prokka/archive/']
 sources = ['v%(version)s.zip']
-checksums = ['0c13dd5621c352633565f5831c4e85ce2e1e400c2f17ba50800282ae121803ff']
 
 dependencies = [
     ('BioPerl', '1.7.8'),
-    ('BLAST+', '2.14.1'),
+    ('BLAST+', '2.16.0'),
     ('Java', '11', '', SYSTEM),
     ('Bio-SearchIO-hmmer', '1.7.3'),
-    ('parallel', '20230722'),
+    ('parallel', '20240722'),
     ('tbl2asn', '20230713'),
+    ('HMMER', '3.4'),
+    ('Infernal', '1.1.5'),
 ]
 
 local_bin_files = ['prokka', 'prokka-cdd_to_hmm', 'prokka-genpept_to_fasta_db', 'prokka-tigrfams_to_hmm',
@@ -36,8 +37,8 @@ local_bin_files = ['prokka', 'prokka-cdd_to_hmm', 'prokka-genpept_to_fasta_db',
 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'],
+    'files': ['bin/%s' % x for x in local_bin_files] + ['db/cm/Bacteria', 'doc/ToDoList.txt'],
+    'dirs': ['bin', 'db',  'db/cm', 'db/genus', 'db/hmm', 'db/kingdom', 'doc'],
 }
 
 sanity_check_commands = [

Diff against prokka-1.14.5-gompi-2022b.eb

easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2022b.eb

diff --git a/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2022b.eb b/easybuild/easyconfigs/p/prokka/prokka-1.15.6-gompi-2024a.eb
index 94b4e5939e..ba7d2cc1d0 100644
--- a/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2022b.eb
+++ b/easybuild/easyconfigs/p/prokka/prokka-1.15.6-gompi-2024a.eb
@@ -8,24 +8,25 @@
 easyblock = 'Tarball'
 
 name = 'prokka'
-version = '1.14.5'
+version = '1.15.6'
 
 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': '2022b'}
+toolchain = {'name': 'gompi', 'version': '2024a'}
 
 source_urls = ['https://github.com/tseemann/prokka/archive/']
 sources = ['v%(version)s.zip']
-checksums = ['0c13dd5621c352633565f5831c4e85ce2e1e400c2f17ba50800282ae121803ff']
 
 dependencies = [
     ('BioPerl', '1.7.8'),
-    ('BLAST+', '2.14.0'),
+    ('BLAST+', '2.16.0'),
     ('Java', '11', '', SYSTEM),
     ('Bio-SearchIO-hmmer', '1.7.3'),
-    ('parallel', '20230722'),
-    ('tbl2asn', '20230713', '-linux64', SYSTEM),
+    ('parallel', '20240722'),
+    ('tbl2asn', '20230713'),
+    ('HMMER', '3.4'),
+    ('Infernal', '1.1.5'),
 ]
 
 local_bin_files = ['prokka', 'prokka-cdd_to_hmm', 'prokka-genpept_to_fasta_db', 'prokka-tigrfams_to_hmm',
@@ -36,8 +37,8 @@ local_bin_files = ['prokka', 'prokka-cdd_to_hmm', 'prokka-genpept_to_fasta_db',
 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'],
+    'files': ['bin/%s' % x for x in local_bin_files] + ['db/cm/Bacteria', 'doc/ToDoList.txt'],
+    'dirs': ['bin', 'db',  'db/cm', 'db/genus', 'db/hmm', 'db/kingdom', 'doc'],
 }
 
 sanity_check_commands = [