docker: tentative fix for transrate

pveber · Feb 5, 2019 · aee6d42 · aee6d42
1 parent c8556cd
commit aee6d42
Showing 1 changed file with 8 additions and 19 deletions.
diff --git a/etc/docker-images/transrate/1.0.3/Dockerfile b/etc/docker-images/transrate/1.0.3/Dockerfile
@@ -3,22 +3,11 @@ FROM pveber/bistro-base:stretch
 RUN apt-get update
 RUN apt-get install -y ruby ruby-dev cmake zlib1g-dev g++
 
-RUN wget http://snap.cs.berkeley.edu/downloads/snap-beta.18-linux.tar.gz && \
-    tar xvfz snap-beta.18-linux.tar.gz && \
-    chmod a+x snap-aligner && \
-    mv snap-aligner /usr/bin && \
-    cd / && rm -rf snap-beta.18-linux.tar.gz
-RUN wget https://github.com/COMBINE-lab/salmon/releases/download/v0.12.0/salmon-0.12.0_linux_x86_64.tar.gz && \
-    tar xvfz salmon-0.12.0_linux_x86_64.tar.gz && \
-    cd salmon-0.12.0_linux_x86_64 && \
-    cp lib/* /usr/lib && \
-    mv bin/salmon /usr/bin && \
-    cd / && rm -rf salmon*
-RUN wget https://github.com/Blahah/transrate-tools/releases/download/v1.0.0/bam-read_v1.0.0_linux.tar.gz && \
-    tar xvfz bam-read_v1.0.0_linux.tar.gz && \
-    rm bam-read_v1.0.0_linux.tar.gz && \
-    chmod a+x bam-read && \
-    mv bam-read /usr/bin && \
-    cd / && rm -rf bam-read_v1.0.0_linux.tar.gz
-
-RUN gem install transrate
+RUN wget https://bintray.com/artifact/download/blahah/generic/transrate-1.0.3-linux-x86_64.tar.gz && \
+    tar xfz transrate-1.0.3-linux-x86_64.tar.gz && \
+    cd transrate-1.0.3-linux-x86_64 && \
+    chmod a+x transrate && \
+    echo '#!/bin/bash\ncd /transrate-1.0.3-linux-x86_64 && ./transrate $@\n' > /usr/bin/transrate && \
+    chmod a+x /usr/bin/transrate
+RUN transrate --install-deps ref
+RUN rm transrate-1.0.3-linux-x86_64/bin/librt.so.1