Merge pull request #5219 from shaneknapp/remove-some-python-from-bio

[DH-178] remove some python packages from bio and timing for R installation

deployments/biology/image/Dockerfile

@@ -169,7 +169,9 @@ USER ${NB_USER}
 COPY environment.yml /tmp/
 COPY infra-requirements.txt /tmp/
 
-RUN mamba env update -p ${CONDA_DIR} -f /tmp/environment.yml && mamba clean -afy
+RUN mamba env update -p ${CONDA_DIR} -f /tmp/environment.yml && \
+    mamba clean -afy
+
 RUN jupyter contrib nbextensions install --sys-prefix --symlink && \
     jupyter nbextensions_configurator enable --sys-prefix
 
@@ -187,7 +189,7 @@ RUN r -e "install.packages('IRkernel', version='1.2')" && \
 # Install R packages, cleanup temp package download location
 COPY install.R /tmp/install.R
 RUN r /tmp/install.R && \
- 	rm -rf /tmp/downloaded_packages/ /tmp/*.rds
+    rm -rf /tmp/downloaded_packages/ /tmp/*.rds
 
 # install bio1b packages
 COPY bio1b-packages.bash /tmp/bio1b-packages.bash

deployments/biology/image/environment.yml

@@ -9,7 +9,7 @@ dependencies:
 - nb_conda_kernels=2.3.1
 
 # Packages from bioconda for IB134L
-- bwa=0.7.12
+# - bwa=0.7.12
 - samtools=1.3.1
 - mafft=7.471
 - emboss=6.6.0
@@ -23,8 +23,8 @@ dependencies:
 - fastqc=0.11.9
 - phyml=3.3.20200621
 - sra-tools=2.11
-- hisat2=2.2.1
-- subread=2.0.1
+# - hisat2=2.2.1
+# - subread=2.0.1
 - plink=1.90b6.21
 
 - syncthing==1.18.6