Update BiG-SCAPE v2 dependency (#328)

* update bs2 version

* change parameter to remove fasttree dependency

* remove fasttree from dependencies

Author: adraismawur

bin/install-nplinker-deps

@@ -144,7 +144,7 @@ echo "🔥 Start installing BigScape ..."
     [[ -d BiG-SCAPE-v2 ]] || git clone -b dev --filter=blob:limit=10m https://github.com/medema-group/BiG-SCAPE.git BiG-SCAPE-v2
     cd BiG-SCAPE-v2
     git config --ad advice.detatchedHead false
-    git checkout 99a4c2e4923bb50e175b2e619c2cee0a14918789 # Commits on Jun 14, 2024
+    git checkout v2.0.0-beta.5 # feb 12, 2025
     pip install click sqlalchemy pyhmmer tqdm matplotlib requests
     chmod 754 bigscape.py
     ln -sf $LIB_PATH/BiG-SCAPE-v2/bigscape.py $PY_PATH/bin/bigscape-v2.py
@@ -153,17 +153,6 @@ echo "🔥 Start installing BigScape ..."
 
 echo -e "✅ BigScape installed successfully\n"
 
-#--- Install FastTree (not support Windows, required by BigScape)
-# http://www.microbesonline.org/fasttree/
-echo "🔥 Start installing FastTree ..."
-    if [[ "$OSTYPE" == "linux"* ]]; then
-        $do_install fasttree
-    elif [[ "$OSTYPE" == "darwin"* ]]; then
-        wget -q --show-progress http://www.microbesonline.org/fasttree/FastTree.c
-        $gcc -DNO_SSE -O3 -finline-functions -funroll-loops -Wall -o $PY_PATH/bin/fasttree FastTree.c -lm
-        rm FastTree.c
-    fi
-echo -e "✅ FastTree installed successfully\n"
 
 #--- Install Hmmer (required by BigScape)
 if ! command -v hmmpress &> /dev/null; then

config/nplinker.toml

@@ -75,10 +75,10 @@ parameters = "version1_parameters_or_version2_parameters"
 # For version 2:
 # --------------
 # BiG-SCAPE v2 has subcommands. NPLinker requires the `cluster` subcommand and its parameters.
-# Required parameters of `cluster` subcommand are: `--mibig_version`, `--include_singletons` and `--gcf_cutoffs`.
-# DO NOT set these parameters: `--pfam_path`, `--inputdir`, `--outputdir`. NPLinker will automatically configure them.
+# Required parameters of `cluster` subcommand are: `--mibig-version`, `--include-singletons` and `--gcf-cutoffs`.
+# DO NOT set these parameters: `--pfam-path`, `--inputdir`, `--outputdir`, `--db-only-output`. NPLinker will automatically configure them.
 # BiG-SCPAPE v2 also runs a `--mix` analysis by default, so you don't need to set this parameter here.
-# An example value could be: "--mibig_version 3.1 --include_singletons --gcf_cutoffs 0.30"
+# An example value could be: "--mibig-version 3.1 --include-singletons --gcf-cutoffs 0.30"
 
 [gnps]
 # Settings for GNPS.

src/nplinker/genomics/bigscape/runbigscape.py

@@ -95,7 +95,14 @@ def run_bigscape(
     if version == "1":
         args.extend(["--pfam_dir", PFAM_PATH])
     elif version == "2":
-        args.extend(["cluster", "--pfam_path", os.path.join(PFAM_PATH, "Pfam-A.hmm")])
+        args.extend(
+            [
+                "cluster",
+                "--pfam-path",
+                os.path.join(PFAM_PATH, "Pfam-A.hmm"),
+                "--db-only-output",
+            ]
+        )
 
     # add input and output paths. these are unchanged
     args.extend(["-i", str(antismash_path), "-o", str(output_path)])