upd plants

dib-lab · Dec 24, 2024 · 2331206 · 2331206
1 parent b3e31f2
commit 2331206
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diff --git a/Makefile b/Makefile
@@ -6,5 +6,11 @@ dist:
 black:
 	python -m black chill_filter_web
 
+dbzip:
+	cd prepare-db && zip -r ../chill-filter-db.zip outputs/* \
+	    downloads/gtdb-rs220-phylum.sig.zip \
+	    downloads/genbank-plants-2024.07.k51.s100_000.sig.zip \
+	    downloads/podar-ref.sig.zip
+
 test:
 	pytest
diff --git a/prepare-db/Snakefile b/prepare-db/Snakefile
@@ -51,7 +51,7 @@ rule plants_animals_and_gtdb:
     input:
         expand('outputs/{g}.k51.100k.sig.zip', g=GENOMES),
         'outputs/all-gtdb-rs220.k51.100k.sig.zip',
-        'downloads/genbank-plants-merged-2024.07.sig.zip',
+        'outputs/genbank-plants-merged-2024.07.sig.zip',
     output:
         'plants+animals+gtdb.mf.csv',
     shell: """
@@ -104,3 +104,12 @@ rule plants_individual_mf:
     shell: """
         sourmash sig collect -F csv {input} -o {output} --abspath
     """
+
+rule plants_merged_all:
+    input:
+        "downloads/genbank-plants-2024.07.k51.s100_000.sig.zip",
+    output:
+        "outputs/genbank-plants-merged-2024.07.sig.zip",
+    shell: """
+        sourmash sig merge --set-name genbank-plants {input} -o {output}
+    """