Updating adding bwa-mem2 wrapper and increasing patch version

Author: skchronicles

docker/genome-seek/trim_map/Dockerfile

@@ -1,34 +1,27 @@
 ############# OVERVIEW #############
 # genome-seek trim_map docker image,
-# uses genome-seek as a base image:
-FROM skchronicles/genome-seek:v0.1.0
+# uses previous version of genome-seek 
+# trim_map (v0.1.0) as a base image:
+FROM skchronicles/genome-seek_trim_map:v0.1.0
 
 # Base image already contains:
-# samblaster and samtools
-# @INSTALLS: 
-#  • fastp, bwa_mem2
+# samblaster, samtools, fastp, bwa_mem2
 WORKDIR /opt2
 
-############## INSTALL #############
-# Install fastp, for more info see:
-# https://github.com/OpenGene/fastp/
-RUN mkdir -p /opt2/fastp/0.23.2/ \
-    && wget http://opengene.org/fastp/fastp.0.23.2 -P /opt2/fastp/0.23.2/ \
-    && mv /opt2/fastp/0.23.2/fastp.0.23.2 /opt2/fastp/0.23.2/fastp \
-    && chmod -R a+rx /opt2/fastp/0.23.2/fastp
-ENV PATH="${PATH}:/opt2/fastp/0.23.2"
-
-# Install bwa_mem2, for more info see:
-# https://github.com/bwa-mem2/bwa-mem2
-RUN mkdir -p /opt2/bwa_mem2/2.2.1/ \
-    && wget https://github.com/bwa-mem2/bwa-mem2/releases/download/v2.2.1/bwa-mem2-2.2.1_x64-linux.tar.bz2 -P /opt2/bwa_mem2/2.2.1/ \
-    && tar -xjvf /opt2/bwa_mem2/2.2.1/bwa-mem2-2.2.1_x64-linux.tar.bz2 -C /opt2/bwa_mem2/2.2.1/ \
-    && rm /opt2/bwa_mem2/2.2.1/bwa-mem2-2.2.1_x64-linux.tar.bz2
-ENV PATH="${PATH}:/opt2/bwa_mem2/2.2.1/bwa-mem2-2.2.1_x64-linux"
-
+############## INSTALL ##############
+# Add bwa-mem2-wrapper to select the
+# correct bwa-mem2 pre-compiled binary
+# for Intel and AMD (Zen4) processors.
+# AMD (Zen4) processors require are not
+# compatible with the AVX-512bw Intel 
+# pre-compiled binary. This wrapper will
+# select the AVX2 binary if run on an
+# AMD processor; otherwise, it will
+# let bwa-mem2 select the best binary.
+ADD bin/bwa-mem2-wrapper /opt2/bwa_mem2/2.2.1/bwa-mem2-2.2.1_x64-linux/bwa-mem2-wrapper
+RUN chmod a+rx /opt2/bwa_mem2/2.2.1/bwa-mem2-2.2.1_x64-linux/bwa-mem2-wrapper
 
 ################ POST #################
 # Add Dockerfile and export env variables
-ADD Dockerfile /opt2/genome-seek_trim_map.dockerfile
-RUN chmod -R a+rX /opt2
-WORKDIR /data2
+ADD Dockerfile /opt2/genome-seek_trim_map_v0.1.1.dockerfile
+WORKDIR /data2

docker/genome-seek/trim_map/README.md

@@ -9,20 +9,20 @@ Directly below are instructions for building an image using the provided Dockerf
 docker image ls
 
 # Build from Dockerfile
-docker build --no-cache -f Dockerfile --tag=genome-seek_trim_map:v0.1.0 .
+docker build --no-cache -f Dockerfile --tag=genome-seek_trim_map:v0.1.1 .
 
 # Testing, take a peek inside
-docker run -ti genome-seek_trim_map:v0.1.0 /bin/bash
+docker run -ti genome-seek_trim_map:v0.1.1 /bin/bash
 
 # Updating Tag  before pushing to DockerHub
-docker tag genome-seek_trim_map:v0.1.0 skchronicles/genome-seek_trim_map:v0.1.0
-docker tag genome-seek_trim_map:v0.1.0 skchronicles/genome-seek_trim_map         # latest
+docker tag genome-seek_trim_map:v0.1.1 skchronicles/genome-seek_trim_map:v0.1.1
+docker tag genome-seek_trim_map:v0.1.1 skchronicles/genome-seek_trim_map         # latest
 
 # Check out new tag(s)
 docker image ls
 
 # Push new tagged image to DockerHub
-docker push skchronicles/genome-seek_trim_map:v0.1.0
+docker push skchronicles/genome-seek_trim_map:v0.1.1
 docker push skchronicles/genome-seek_trim_map:latest
 ```
 
@@ -31,7 +31,7 @@ docker push skchronicles/genome-seek_trim_map:latest
 Scan your image for known vulnerabilities:
 
 ```bash
-docker scan genome-seek_trim_map:v0.1.0
+docker scan genome-seek_trim_map:v0.1.1
 ```
 
 > **Please Note**: Any references to `skchronicles` should be replaced your username if you would also like to push the image to a non-org account.