Update Dockerfile to include all dbs

Dockerfile

@@ -25,9 +25,29 @@ RUN conda create --name rgi --channel conda-forge --channel bioconda rgi
 RUN mkdir -p /card_data
 WORKDIR /card_data
 RUN wget -O data.tar.bz2 https://card.mcmaster.ca/latest/data && \
-        tar xvf data.tar.bz2 && pwd && ls
-# install database
-SHELL ["conda", "run", "-n", "rgi", "rgi", "load", "-i", "/card_data/card.json"]
+        mkdir -p canonical &&  tar xf data.tar.bz2 -C canonical
+
+# download wildcard data (modified from @nebfield)
+RUN wget -O wildcard_data.tar.bz2 https://card.mcmaster.ca/latest/variants && \
+    mkdir -p wildcard && \
+    tar xf wildcard_data.tar.bz2 -C wildcard && \
+        gunzip wildcard/*.gz
+
+# install CARD database
+SHELL ["conda", "run", "-n", "rgi", "card_annotation", "-i",  "canonical/card.json", ">", "card_annotation.log", "2>&1"]
+SHELL ["conda", "run", "-n", "rgi", "rgi", "load", "-i", "caonical/card.json", "--card_annotation", "card_database_*.fasta"]
+
+# install WILDCARD database
+# version number not in downloaded data so can't do this in a way that will
+# automatically be entered
+SHELL ["conda", "run", "-n", "rgi", "rgi", "wildcard_annotation", "-i", "wildcard", "--card_json", "canonical/card.json", "-v", "docker_version_number", ">", "wildcard_annotation.log", "2>&1"]
+SHELL ["conda", "run", "-n", "rgi", "rgi", "load", "--wildcard_annotation", "wildcard_database*", "--wildcard_index", "wildcard/index-for-model-sequences.txt", "--card_annotation", "card_database*"]
+
+# install kmer pathogen-of-origin database
+SHELL ["conda", "run", "-n", "rgi", "rgi", "load", "--kmer_database", "wildcard/61_kmer_db.json", "--amr_kmers", "wildcard/all_amr_61mers.txt", "--kmer_size", "61", "--debug", ">", "kmer_load.61.log", "2>&1"]
+
+# Remove non-loaded databases to reduce container size
+RUN cp *.log /data && rm -rf /card_data
 
 WORKDIR /data
 # set rgi executable as cmd to allow overriding