From 1c1182a6ae63c7857318ad8adec3ea0fc2e232f9 Mon Sep 17 00:00:00 2001
From: Eva Gunawan <124393795+evagunawan@users.noreply.github.com>
Date: Thu, 30 Nov 2023 10:47:05 -0600
Subject: [PATCH] Update Dockerfile

Added update TBDB
---
 tbprofiler/5.0.1/Dockerfile | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/tbprofiler/5.0.1/Dockerfile b/tbprofiler/5.0.1/Dockerfile
index 50c47d37e..5d6bcae47 100644
--- a/tbprofiler/5.0.1/Dockerfile
+++ b/tbprofiler/5.0.1/Dockerfile
@@ -39,14 +39,15 @@ ARG MAMBA_DOCKERFILE_ACTIVATE=1
 
 # Version of database can be confirmed at /opt/conda/share/tbprofiler/tbdb.version.json
 # can also run 'tb-profiler list_db' to find the same version info
-# In 5.0.1 updating_tbdb does not work through this --commit but list_db produces correct version
-# RUN tb-profiler update_tbdb --commit ${TBDB_VER}
+# In 5.0.1 updating_tbdb does not work with tb-profiler update_tbdb --commit ${TBDB_VER}
+RUN tb-profiler update_tbdb
 
 WORKDIR /data
 
 # hardcode 'base' env bin into PATH, so conda env does not have to be "activated" at run time
 ENV PATH="/opt/conda/bin:${PATH}"
 
+# Added command to bring help menu up upon running container.
 CMD "tb-profiler"
 
 # test stage
@@ -57,4 +58,4 @@ WORKDIR /tests
 # download some TB FASTQs and run through tb-profiler
 RUN wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR166/009/ERR1664619/ERR1664619_1.fastq.gz && \
     wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR166/009/ERR1664619/ERR1664619_2.fastq.gz && \
-    tb-profiler profile -1 ERR1664619_1.fastq.gz -2 ERR1664619_2.fastq.gz -t 2 -p ERR1664619 --txt
\ No newline at end of file
+    tb-profiler profile -1 ERR1664619_1.fastq.gz -2 ERR1664619_2.fastq.gz -t 2 -p ERR1664619 --txt