adding SciServer image commits

Dockerfile

@@ -7,26 +7,11 @@ ENV PATH /opt/conda/bin:$PATH
 # Make RUN commands use `bash --login` (always source ~/.bashrc on each RUN)
 SHELL ["/bin/bash", "--login", "-c"]
 
-# configure user/group permissions
-# ARG USER_ID
-# ARG GROUP_ID
-# ARG ENVIRONMENT
-
-# RUN if [[ $ENVIRONMENT != "WIN" ]]; then addgroup --gid $GROUP_ID user; else addgroup --gid 1000 user; fi 
-# RUN if [[ $ENVIRONMENT != "WIN" ]]; then adduser --disabled-password --gecos '' --uid $USER_ID --gid $GROUP_ID user; else adduser --disabled-password --gecos '' --uid 1000 --gid 1000 user; fi 
-
 # install apt depedencies
 RUN apt-get update \
-    && apt-get install -y git texlive-xetex curl apt-transport-https ca-certificates wget unzip bzip2 \
-    && update-ca-certificates
-
-# install docker for sibling container usage: https://medium.com/@andreacolangelo/sibling-docker-container-2e664858f87a
-RUN curl -sSL https://get.docker.com/ | sh \
-    && usermod -aG docker root
-#    && usermod -aG docker user
-
-# free up space in image
-RUN apt-get -qq -y remove curl \
+    && mkdir /usr/share/man/man1 \
+    && apt-get install --no-install-recommends -y git texlive-xetex apt-transport-https ca-certificates wget unzip bzip2 openjdk-11-jdk-headless \
+    && update-ca-certificates \
     && apt-get -qq -y autoremove \
     && apt-get autoclean \
     && rm -rf /var/lib/apt/lists/* /var/log/dpkg.log 
@@ -36,22 +21,19 @@ RUN conda install -y python=3 \
     && conda update -y conda \
     && conda clean --all --yes
 
-# configure directory structure exactly as it is on SciServer for ease of transition
-WORKDIR /home/idies/workspace/covid19/code
-
-# link global conda to expected sciserver location
-RUN ln -s /opt/conda/ /home/idies/workspace/covid19/miniconda3
-
+RUN mkdir /opt/nCovIllumina
+WORKDIR /opt/nCovIllumina
 # clone VCF IGV repo and install local IGV
 RUN git clone https://github.com/mkirsche/vcfigv \
     && wget https://data.broadinstitute.org/igv/projects/downloads/2.8/IGV_2.8.10.zip -P vcfigv \
     && unzip -d vcfigv vcfigv/IGV_2.8.10.zip \
-    && rm vcfigv/IGV_2.8.10.zip
+    && rm vcfigv/IGV_2.8.10.zip \
+    && git clone --recurse-submodules https://github.com/connor-lab/ncov2019-artic-nf \
+    && git clone https://github.com/mkirsche/VariantValidator.git \
+    && git clone --recurse-submodules https://github.com/artic-network/artic-ncov2019 \
+    && git clone https://github.com/artic-network/primer-schemes
 
-# install nextflow pipeline
-WORKDIR /home/idies/workspace/covid19/code/
-RUN git clone --recurse-submodules https://github.com/connor-lab/ncov2019-artic-nf \
-    && conda env create -f ncov2019-artic-nf/environments/illumina/environment.yml
+RUN conda env create -f ncov2019-artic-nf/environments/illumina/environment.yml
 
 # install nextstrain pipeline
 WORKDIR /home/idies/workspace/covid19/code/
@@ -65,26 +47,17 @@ RUN git clone https://github.com/cov-lineages/pangolin.git \
     && conda activate pangolin \
     && cd pangolin && python setup.py install
 
-# install pipeline code
-# WORKDIR /home/idies/workspace/covid19/code
-# RUN git clone --recurse-submodules https://github.com/mkirsche/nCovIllumina
-WORKDIR /home/idies/workspace/covid19/code/nCovIllumina
-RUN conda install -c bioconda -y nextflow
-COPY . .
+COPY environment.yml .
 RUN conda env create -f environment.yml
-RUN git clone https://github.com/mkirsche/VariantValidator.git \
-    && git clone --recurse-submodules https://github.com/artic-network/artic-ncov2019 \
-    && git clone https://github.com/artic-network/primer-schemes
 
-# configure bash environment
-ENV PATH="/home/idies/workspace/covid19/code/jdk-14/bin:${PATH}"
-RUN cat /home/idies/workspace/covid19/code/nCovIllumina/bashrc >> ~/.bashrc
+RUN conda install -c bioconda -y nextflow matplotlib
+
+COPY . .
 
-# install missing dependencies
-RUN source ~/.bashrc \
-    && conda activate artic-ncov2019-illumina \
-    && conda install -y -c bioconda matplotlib
+RUN useradd idies \
+    && mkdir -p /home/idies/workspace \
+    && chown -R idies:idies /home/idies \
+    && chown -R idies:idies /opt/nCovIllumina
 
-# set default working directory
-WORKDIR /home/idies/workspace/covid19/code/nCovIllumina
-#USER user
+COPY bashrc /home/idies/.bashrc
+USER idies

bashrc

@@ -21,14 +21,5 @@ source /opt/conda/etc/profile.d/conda.sh
 
 conda activate artic-ncov2019-illumina
 
-# compile java libraries
-javac "/home/idies/workspace/covid19/code/nCovIllumina/VariantValidator/src"/*.java
-javac "/home/idies/workspace/covid19/code/vcfigv/src"/*.java
-
-# deal with primer scheme rename bugs
-#primer_schemes=/home/idies/workspace/covid19/code/nCovIllumina/artic-ncov2019/primer_schemes
-
-#samtools faidx "$primer_schemes/SARS-CoV-2/V3/nCoV-2019.reference.fasta"
-#for f in "$primer_schemes/SARS-CoV-2/V3/"*; do ln -sf "$f" "${f/nCoV-2019/SARS-CoV-2}"; done
-#ln -sf "$primer_schemes/SARS-CoV-2" "$primer_schemes/nCoV-2019"
-#ln -sf "$primer_schemes" "/home/idies/workspace/covid19/code/nCovIllumina/artic-ncov2019/primer-schemes"
+javac "/opt/nCovIllumina/VariantValidator/src"/*.java
+javac "/opt/nCovIllumina/vcfigv/src"/*.java

pipeline.sh

@@ -10,6 +10,7 @@ else
 fi
 
 # Load parameters from config
+source $BINDIR/bashrc
 source $BINDIR/config/illumina.txt
 
 # Set up script parameters based on config setup
@@ -63,6 +64,7 @@ then
   javac $BINDIR/src/ParseIvarConfig.java
   extraargs=`java -cp $BINDIR/src ParseIvarConfig $BINDIR/config/illumina.txt`
   echo 'Running ivar'
+  conda activate artic-ncov2019-illumina
   $BINDIR/src/ivar.sh $FILTEREDINPUTDIR $extraargs
 fi
 
@@ -71,7 +73,7 @@ fi
 ## Call variants 
 
 # Load necessary conda environment
-source /home/idies/workspace/covid19/code/nCovIllumina/bashrc
+
 conda activate ncov_illumina
 
 # Call variants

src/ivar.sh

@@ -8,6 +8,4 @@ DATADIR=$1
 #fi
 EXTRAARGS=`echo "${@:2}"`
 echo 'Extra args: ' $EXTRAARGS
-source /home/idies/workspace/covid19/code/nCovIllumina/bashrc
-conda activate artic-ncov2019-illumina
-nextflow run connor-lab/ncov2019-artic-nf --with-docker ncovillumina --illumina --prefix test --directory $DATADIR $EXTRAARGS
+nextflow run connor-lab/ncov2019-artic-nf --illumina --prefix test --directory $DATADIR $EXTRAARGS