fix: consolidate docker

CCBR · May 30, 2024 · 5d83d8e · 5d83d8e
1 parent 8bdd86d
commit 5d83d8e
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Showing 4 changed files with 12 additions and 52 deletions.
diff --git a/docker/hmftools/Dockerfile b/docker/hmftools/Dockerfile
diff --git a/docker/hmftools/build.sh b/docker/hmftools/build.sh
diff --git a/docker/hmftools/meta.yml b/docker/hmftools/meta.yml
diff --git a/docker/logan_base/Dockerfile b/docker/logan_base/Dockerfile
@@ -213,6 +213,18 @@ RUN wget -O muse_2.0.4.tar.gz https://github.com/wwylab/MuSE/archive/refs/tags/v
 
 ENV PATH="/opt2/MuSE:$PATH"
 
+# HMFtools for PURPLE/COBALT/AMBER
+RUN wget https://github.com/hartwigmedical/hmftools/releases/download/amber-v4.0/amber-4.0.jar \
+    && wget https://github.com/hartwigmedical/hmftools/releases/download/cobalt-v1.16/cobalt_v1.16.jar \
+    && wget https://github.com/hartwigmedical/hmftools/releases/download/purple-v4.0/purple_v4.0.jar \
+    && wget https://github.com/hartwigmedical/hmftools/releases/download/sage-v3.4/sage_v3.4.jar \ 
+    && mkdir hmftools \
+    && mv amber-4.0.jar hmftools/amber.jar \
+    && mv cobalt_v1.16.jar hmftools/cobalt.jar \
+    && mv purple_v4.0.jar hmftools/purple.jar \
+    && mv sage.v3.4.jar hmftools/sage.jar \
+    && chmod a+x hmftools/amber.jar
+ENV PATH="/opt2/hmftools:$PATH"
 
 # Add Dockerfile and argparse.bash script
 # and export environment variables