From c3c46fd0cb4ae8533dc825fdb7850c23f52f4ad8 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Thu, 16 Jan 2025 14:23:51 +0100
Subject: [PATCH 1/3] adding easyconfigs: vRhyme-1.1.0-foss-2023a.eb

---
 .../v/vRhyme/vRhyme-1.1.0-foss-2023a.eb       | 47 +++++++++++++++++++
 1 file changed, 47 insertions(+)
 create mode 100644 easybuild/easyconfigs/v/vRhyme/vRhyme-1.1.0-foss-2023a.eb

diff --git a/easybuild/easyconfigs/v/vRhyme/vRhyme-1.1.0-foss-2023a.eb b/easybuild/easyconfigs/v/vRhyme/vRhyme-1.1.0-foss-2023a.eb
new file mode 100644
index 00000000000..25e163336ce
--- /dev/null
+++ b/easybuild/easyconfigs/v/vRhyme/vRhyme-1.1.0-foss-2023a.eb
@@ -0,0 +1,47 @@
+easyblock = 'PythonBundle'
+
+name = 'vRhyme'
+version = '1.1.0'
+
+homepage = 'https://github.com/AnantharamanLab/vRhyme'
+description = """vRhyme is a multi-functional tool for binning virus genomes from metagenomes.
+vRhyme functions by utilizing coverage variance comparisons and supervised machine learning classification
+of sequence features to construct viral metagenome-assembled genomes (vMAGs)."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('scikit-learn', '1.3.1'),
+    ('numba', '0.58.1'),
+    ('Pysam', '0.22.0'),
+    ('networkx', '3.1'),
+    ('MMseqs2', '15-6f452'),
+    ('SAMtools', '1.18'),
+    ('prodigal', '2.6.3'),
+    ('Mash', '2.3'),
+    ('MUMmer', '4.0.0rc1'),
+    ('Bowtie2', '2.5.1'),
+    ('BWA', '0.7.18'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    (name, version, {
+        'modulename': 'vRhyme',
+        'preinstallopts': "gunzip vRhyme/models/vRhyme_machine_model_ET.sav.gz && ",
+        'source_tmpl': 'v%(version)s.tar.gz',
+        'source_urls': ['https://github.com/AnantharamanLab/vRhyme/archive'],
+        'checksums': ['ffc8b7b7f976d251e5f42d41ef88f8a9bc3d3b6044fc443f31625a5feff83985'],
+    }),
+]
+
+sanity_check_commands = [
+    'vRhyme --help',
+    '! test_vRhyme.py | grep "Not Found"',
+]
+
+moduleclass = 'bio'

From ea0ef5d5368f0283d2d0287cd4566d63ade8f17b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Thu, 16 Jan 2025 15:33:47 +0100
Subject: [PATCH 2/3] Use correct version of MMseqs2

---
 easybuild/easyconfigs/v/vRhyme/vRhyme-1.1.0-foss-2023a.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/v/vRhyme/vRhyme-1.1.0-foss-2023a.eb b/easybuild/easyconfigs/v/vRhyme/vRhyme-1.1.0-foss-2023a.eb
index 25e163336ce..9ab60f3e81e 100644
--- a/easybuild/easyconfigs/v/vRhyme/vRhyme-1.1.0-foss-2023a.eb
+++ b/easybuild/easyconfigs/v/vRhyme/vRhyme-1.1.0-foss-2023a.eb
@@ -17,7 +17,7 @@ dependencies = [
     ('numba', '0.58.1'),
     ('Pysam', '0.22.0'),
     ('networkx', '3.1'),
-    ('MMseqs2', '15-6f452'),
+    ('MMseqs2', '14-7e284'),
     ('SAMtools', '1.18'),
     ('prodigal', '2.6.3'),
     ('Mash', '2.3'),

From 8601e2b9cbb172d0aa0292c9500852993883f849 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Thu, 16 Jan 2025 16:03:18 +0100
Subject: [PATCH 3/3] stick to BWA 0.7.17

---
 easybuild/easyconfigs/v/vRhyme/vRhyme-1.1.0-foss-2023a.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/v/vRhyme/vRhyme-1.1.0-foss-2023a.eb b/easybuild/easyconfigs/v/vRhyme/vRhyme-1.1.0-foss-2023a.eb
index 9ab60f3e81e..09fddc1862c 100644
--- a/easybuild/easyconfigs/v/vRhyme/vRhyme-1.1.0-foss-2023a.eb
+++ b/easybuild/easyconfigs/v/vRhyme/vRhyme-1.1.0-foss-2023a.eb
@@ -23,7 +23,7 @@ dependencies = [
     ('Mash', '2.3'),
     ('MUMmer', '4.0.0rc1'),
     ('Bowtie2', '2.5.1'),
-    ('BWA', '0.7.18'),
+    ('BWA', '0.7.17'),
 ]
 
 use_pip = True