From 4014f0f3e71193abc524084eb4983508dfeccc31 Mon Sep 17 00:00:00 2001
From: jvhagey <jvhagey@gmail.com>
Date: Fri, 30 Aug 2024 11:23:18 -0400
Subject: [PATCH] update shigapass

---
 shigapass/1.5.0/Dockerfile | 12 +++++++++---
 shigapass/1.5.0/README.md  |  4 +++-
 2 files changed, 12 insertions(+), 4 deletions(-)

diff --git a/shigapass/1.5.0/Dockerfile b/shigapass/1.5.0/Dockerfile
index 34ea80536..ea88bd533 100644
--- 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-${SHIGAPASS_VER}/SCRIPT/ShigaPass_DataBases -u -k
\ No newline at end of file
+RUN ShigaPass.sh -l /ShigaPass-${SHIGAPASS_VER}/Example/Input/ShigaPass_test.txt -o ShigaPass_Results -p ${DB_PATH}
\ No newline at end of file
diff --git a/shigapass/1.5.0/README.md b/shigapass/1.5.0/README.md
index 3a2e4ba67..6f668108d 100644
--- 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
 ```
\ No newline at end of file