update shigapass

StaPH-B · Aug 30, 2024 · 4014f0f · 4014f0f
1 parent 6ed5fca
commit 4014f0f
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Showing 2 changed files with 12 additions and 4 deletions.
diff --git a/shigapass/1.5.0/Dockerfile b/shigapass/1.5.0/Dockerfile
@@ -38,11 +38,19 @@ RUN wget https://github.com/imanyass/ShigaPass/archive/refs/tags/v${SHIGAPASS_VE
     chmod +x /ShigaPass-${SHIGAPASS_VER}/SCRIPT/ShigaPass.sh && \
     mkdir /data
 
+#creating variable for referencing database
+ENV DB_PATH=/ShigaPass-${SHIGAPASS_VER}/SCRIPT/ShigaPass_DataBases/
+
 # 'ENV' instructions set environment variables that persist from the build into the resulting image
 # Use for e.g. $PATH and locale settings for compatibility with Singularity
 ENV PATH="/ncbi-blast-${BLAST_VER}+/bin/:/ShigaPass-${SHIGAPASS_VER}/SCRIPT:$PATH" \
  LC_ALL=C
 
+# running test to index the database
+RUN gunzip /ShigaPass-${SHIGAPASS_VER}/Example/Input/*.gz && \
+sed -i "s/^/\/ShigaPass-${SHIGAPASS_VER}\//" /ShigaPass-${SHIGAPASS_VER}/Example/Input/ShigaPass_test.txt && \
+ShigaPass.sh -l /ShigaPass-${SHIGAPASS_VER}/Example/Input/ShigaPass_test.txt -o ShigaPass_Results -p ${DB_PATH} -u
+
 # 'CMD' instructions set a default command when the container is run. This is typically 'tool --help.'
 CMD [ "ShigaPass.sh" ]
 
@@ -60,6 +68,4 @@ RUN ShigaPass.sh -h && \
  ShigaPass.sh -v
 
 # Testing a script - need to unzip the test files and correct the path for the container
-RUN gunzip /ShigaPass-${SHIGAPASS_VER}/Example/Input/*.gz && \
-sed -i "s/^/\/ShigaPass-${SHIGAPASS_VER}\//" /ShigaPass-${SHIGAPASS_VER}/Example/Input/ShigaPass_test.txt && \
-ShigaPass.sh -l /ShigaPass-${SHIGAPASS_VER}/Example/Input/ShigaPass_test.txt -o ShigaPass_Results -p /ShigaPass-${SHIGAPASS_VER}/SCRIPT/ShigaPass_DataBases -u -k
+RUN ShigaPass.sh -l /ShigaPass-${SHIGAPASS_VER}/Example/Input/ShigaPass_test.txt -o ShigaPass_Results -p ${DB_PATH}
diff --git a/shigapass/1.5.0/README.md b/shigapass/1.5.0/README.md
@@ -29,8 +29,10 @@ Additional information:
 
 Full documentation: https://github.com/imanyass/ShigaPass
 
+Included Database: Found at `/ShigaPass-${version}/SCRIPT/ShigaPass_DataBases/` so for v1.5.0 use `-p /ShigaPass-1.5.0/SCRIPT/ShigaPass_DataBases/`
+
 ## Example Usage
 
 ```bash
-ShigaPass.sh -l ShigaPass_test.txt -o ShigaPass_Results -p ShigaPass_DataBases -u -k
+ShigaPass.sh -l ShigaPass_test.txt -o ShigaPass_Results -p /ShigaPass-1.5.0/SCRIPT/ShigaPass_DataBases/ -u -k
 ```