remove gatk3-register command (#496)

* remove gatk3-register command * remove gatk3 resources
Clinical-Genomics · Nov 10, 2020 · 22c48f6 · 22c48f6
1 parent 6ac9761
commit 22c48f6
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diff --git a/BALSAMIC/assets/GenomeAnalysisTK.jar b/BALSAMIC/assets/GenomeAnalysisTK.jar
diff --git a/BALSAMIC/assets/gatk_3.8.tar.bz2 b/BALSAMIC/assets/gatk_3.8.tar.bz2
diff --git a/BALSAMIC/containers/Dockerfile.develop b/BALSAMIC/containers/Dockerfile.develop
@@ -30,7 +30,6 @@ RUN mkdir -p /git_repos; \
     conda env create --file BALSAMIC/conda/varcall_py27.yaml -n varcall_py27 && \
     conda env create --file BALSAMIC/conda/varcall_py36.yaml -n varcall_py36 && \
     source activate varcall_py36 && \
-    gatk3-register BALSAMIC/assets/GenomeAnalysisTK.jar && \
     ln -s /usr/local/miniconda/envs/varcall_py36/lib/libreadline.so.7.0 /usr/local/miniconda/envs/varcall_py36/lib/libreadline.so.6 && \
     ln -s /usr/local/miniconda/envs/varcall_py36/lib/libreadline.so.7.0 /usr/local/miniconda/envs/varcall_py36/lib/libreadline.so.6.0 && \
     source deactivate && \

diff --git a/BALSAMIC/containers/Dockerfile.latest b/BALSAMIC/containers/Dockerfile.latest
@@ -30,7 +30,6 @@ RUN mkdir -p /git_repos; \
     conda env create --file BALSAMIC/conda/varcall_py27.yaml -n varcall_py27 && \
     conda env create --file BALSAMIC/conda/varcall_py36.yaml -n varcall_py36 && \
     source activate varcall_py36 && \
-    gatk3-register BALSAMIC/assets/GenomeAnalysisTK.jar && \
     ln -s /usr/local/miniconda/envs/varcall_py36/lib/libreadline.so.7.0 /usr/local/miniconda/envs/varcall_py36/lib/libreadline.so.6 && \
     ln -s /usr/local/miniconda/envs/varcall_py36/lib/libreadline.so.7.0 /usr/local/miniconda/envs/varcall_py36/lib/libreadline.so.6.0 && \
     source deactivate && \

diff --git a/BALSAMIC/containers/Dockerfile.release b/BALSAMIC/containers/Dockerfile.release
@@ -30,7 +30,6 @@ RUN mkdir -p /git_repos; \
     conda env create --file BALSAMIC/conda/varcall_py27.yaml -n varcall_py27 && \
     conda env create --file BALSAMIC/conda/varcall_py36.yaml -n varcall_py36 && \
     source activate varcall_py36 && \
-    gatk3-register BALSAMIC/assets/GenomeAnalysisTK.jar && \
     ln -s /usr/local/miniconda/envs/varcall_py36/lib/libreadline.so.7.0 /usr/local/miniconda/envs/varcall_py36/lib/libreadline.so.6 && \
     ln -s /usr/local/miniconda/envs/varcall_py36/lib/libreadline.so.7.0 /usr/local/miniconda/envs/varcall_py36/lib/libreadline.so.6.0 && \
     source deactivate && \