Merge pull request #6 from mcveanlab/paper_revisions

Paper revisions

.gitignore

@@ -53,4 +53,6 @@ example*/
 *.tex
 *.fa
 *.gfa
-*.gfa
+*.zip
+cromwell/docker/corticall/corticall.jar
+cromwell/go.sh

build.xml

@@ -4,8 +4,8 @@
                       University of Oxford
   -->
 
-<project name="cortexjdk" default="dist" xmlns:ivy="antlib:org.apache.ivy.ant">
-    <description>Compile and distribute CortexJDK</description>
+<project name="corticall" default="dist" xmlns:ivy="antlib:org.apache.ivy.ant">
+    <description>Compile and distribute Corticall</description>
 
     <property name="src.dir" value="public/java" />
     <property name="src.R.dir" value="public/R" />
@@ -34,7 +34,7 @@
     <target name="install-ivy" unless="skip.download" description="install ivy">
         <mkdir dir="${ivy.jar.dir}"/>
 
-        <get src="http://repo1.maven.org/maven2/org/apache/ivy/ivy/${ivy.install.version}/ivy-${ivy.install.version}.jar"
+        <get src="https://repo1.maven.org/maven2/org/apache/ivy/ivy/${ivy.install.version}/ivy-${ivy.install.version}.jar"
              dest="${ivy.jar.file}" usetimestamp="true"/>
 
         <path id="ivy.lib.path">
@@ -92,7 +92,7 @@
             <fileset dir="${src.html.dir}" />
         </copy>
 
-        <jar jarfile="${jars.dir}/cortexjdk.jar">
+        <jar jarfile="${jars.dir}/corticall.jar">
             <fileset dir="${build.dir}">
                 <include name="**/*.class" />
                 <include name="**/*.properties" />
@@ -111,7 +111,7 @@
         </jar>
     </target>
 
-    <!-- Prepare to make a jar file with all the CortexJDK code and dependencies -->
+    <!-- Prepare to make a jar file with all the Corticall code and dependencies -->
     <target name="stage" description="stage files for distribution">
         <mkdir dir="${staging.dir}" />
 
@@ -120,11 +120,11 @@
         </unjar>
     </target>
 
-    <!-- Create a single executable jar with all of the CortexJDK and dependency code wrapped up -->
+    <!-- Create a single executable jar with all of the Corticall and dependency code wrapped up -->
     <target name="dist" depends="tidy,compile,stage" description="bundle up an executable for distribution">
         <mkdir dir="${dist.dir}" />
 
-        <jar jarfile="${dist.dir}/cortexjdk.jar">
+        <jar jarfile="${dist.dir}/corticall.jar">
             <fileset dir="${build.dir}">
                 <include name="**/*.properties" />
                 <include name="**/*.R" />

cromwell/docker/Makefile

@@ -0,0 +1,9 @@
+MODULES = lr-align lr-asm lr-bri lr-c3poa lr-cloud-downloader lr-finalize lr-gatk lr-guppy lr-longshot lr-metrics lr-ont lr-pb lr-peregrine lr-sv lr-svim lr-utils racon sr-utils
+
+all:
+	for dir in $(MODULES); do \
+		echo begin $$dir; \
+		(cd $$dir; ${MAKE}); \
+		echo end $$dir; \
+		echo ==========; \
+	done

cromwell/docker/align/Dockerfile

@@ -0,0 +1,16 @@
+FROM continuumio/miniconda3
+
+MAINTAINER Kiran V Garimella
+
+# copy other resources
+COPY ./environment.yml /
+
+# install conda packages
+RUN conda env create -f /environment.yml && conda clean -a
+ENV PATH=/opt/conda/envs/align/bin/:${PATH}
+#ENV PATH=/opt/conda/envs/align/bin/:/root/google-cloud-sdk/bin/:${PATH}
+
+# install packages
+RUN apt update
+RUN apt-get install -y --no-install-recommends curl \
+    && rm -rf /var/lib/apt/lists/*

cromwell/docker/align/Makefile

@@ -0,0 +1,10 @@
+VERSION = 0.1.0
+TAG = quay.io/corticall/align:$(VERSION)
+
+all: build push
+
+build:
+	docker build -t $(TAG) .
+
+push:
+	docker push $(TAG)

cromwell/docker/align/environment.yml

@@ -0,0 +1,8 @@
+name: align
+channels:
+  - defaults
+  - conda-forge
+  - bioconda
+dependencies:
+  - samtools
+  - bwa

cromwell/docker/cloud-downloader/Dockerfile

@@ -0,0 +1,22 @@
+# This image contains dependencies used by the cloud downloader system.
+
+FROM continuumio/miniconda3
+
+MAINTAINER Kiran V Garimella
+
+# copy other resources
+COPY ./environment.yml /
+
+# install conda packages
+RUN conda env create -f /environment.yml && conda clean -a
+ENV PATH=/opt/conda/envs/lr-cloud-downloader/bin/:/root/google-cloud-sdk/bin/:${PATH}
+
+# install python2.7 (required by gsutil), then gcloud sdk
+RUN apt-get -qqy update --fix-missing && \
+    apt-get -qqy dist-upgrade && \
+    apt-get -qqy install --no-install-recommends \
+    			 curl \
+    			 pigz \
+    			 python2.7 && \
+    curl https://sdk.cloud.google.com | bash && \
+    gsutil

cromwell/docker/cloud-downloader/Makefile

@@ -0,0 +1,16 @@
+VERSION = 0.2.1
+TAG1 = quay.io/broad-long-read-pipelines/lr-cloud-downloader:$(VERSION)
+TAG2 = quay.io/broad-long-read-pipelines/lr-cloud-downloader:latest
+TAG3 = us.gcr.io/broad-dsp-lrma/lr-cloud-downloader:$(VERSION)
+TAG4 = us.gcr.io/broad-dsp-lrma/lr-cloud-downloader:latest
+
+all: build push
+
+build:
+	docker build -t $(TAG1) -t $(TAG2) -t $(TAG3) -t $(TAG4) .
+
+push:
+	docker push $(TAG1)
+	docker push $(TAG2)
+	docker push $(TAG3)
+	docker push $(TAG4)

cromwell/docker/cloud-downloader/environment.yml

@@ -0,0 +1,10 @@
+name: lr-cloud-downloader
+channels:
+  - defaults
+  - conda-forge
+  - bioconda
+dependencies:
+  - sra-tools=2.9.1
+  - entrez-direct=7.70
+  - parallel-fastq-dump=0.6.3
+  - readline=6.2

cromwell/docker/corticall/Dockerfile

@@ -0,0 +1,21 @@
+FROM continuumio/miniconda3
+
+MAINTAINER Kiran V Garimella
+
+# copy other resources
+COPY ./environment.yml /
+
+# install conda packages
+RUN conda env create -f /environment.yml && conda clean -a
+ENV PATH=/opt/conda/envs/corticall/bin/:/root/google-cloud-sdk/bin/:${PATH}
+
+# install packages
+RUN apt update
+RUN apt-get install -y --no-install-recommends curl git \
+    && rm -rf /var/lib/apt/lists/*
+
+# install gsutil
+RUN curl https://sdk.cloud.google.com | bash
+
+# install Corticall
+COPY corticall.jar /usr/local/bin/corticall.jar

cromwell/docker/corticall/Makefile

@@ -0,0 +1,11 @@
+VERSION = 0.1.9
+TAG = quay.io/corticall/corticall:$(VERSION)
+
+all: build push
+
+build:
+	cp ../../../dist/corticall.jar .
+	docker build -t $(TAG) .
+
+push:
+	docker push $(TAG)

cromwell/docker/corticall/environment.yml

@@ -0,0 +1,11 @@
+name: corticall
+channels:
+  - defaults
+  - conda-forge
+  - bioconda
+dependencies:
+  - java-jdk
+  - ant
+  - mccortex
+  - cd-hit
+  - samtools

cromwell/docker/gridss/Dockerfile

@@ -0,0 +1,7 @@
+FROM gridss/gridss:latest
+
+MAINTAINER Kiran V Garimella
+
+# reset entrypoint
+ENTRYPOINT []
+CMD ["/bin/bash"]

cromwell/docker/gridss/Makefile

@@ -0,0 +1,10 @@
+VERSION = 0.1.0
+TAG = quay.io/corticall/gridss:$(VERSION)
+
+all: build push
+
+build:
+	docker build -t $(TAG) .
+
+push:
+	docker push $(TAG)

cromwell/docker/gridss/environment.yml

@@ -0,0 +1,15 @@
+name: sv
+channels:
+  - defaults
+  - conda-forge
+  - bioconda
+dependencies:
+  - samtools
+  - pysam
+  - numpy
+  - delly
+  - manta
+  - lumpy-sv
+  - gridss
+  - bcftools
+  - gatk4

cromwell/docker/mccortex/Dockerfile

@@ -0,0 +1,24 @@
+FROM continuumio/miniconda3
+
+MAINTAINER Kiran V Garimella
+
+# copy other resources
+COPY ./environment.yml /
+
+# install conda packages
+RUN conda env create -f /environment.yml && conda clean -a
+ENV PATH=/opt/conda/envs/mccortex/bin/:/root/google-cloud-sdk/bin/:${PATH}
+
+# install packages
+RUN apt update
+RUN apt-get install -y --no-install-recommends curl make gcc g++ autoconf libc6-dev zlib1g-dev \
+    && rm -rf /var/lib/apt/lists/*
+
+# install gsutil
+RUN curl https://sdk.cloud.google.com | bash
+
+# install cd-hit
+RUN git clone https://github.com/weizhongli/cdhit.git \
+    && cd cdhit \
+    && make MAX_SEQ=10000000 \
+    && make install

cromwell/docker/mccortex/Makefile

@@ -0,0 +1,10 @@
+VERSION = 0.3.1
+TAG = quay.io/corticall/mccortex:$(VERSION)
+
+all: build push
+
+build:
+	docker build -t $(TAG) .
+
+push:
+	docker push $(TAG)

cromwell/docker/mccortex/environment.yml

@@ -0,0 +1,8 @@
+name: mccortex
+channels:
+  - defaults
+  - conda-forge
+  - bioconda
+dependencies:
+  - samtools
+  - mccortex

cromwell/docker/metrics/Dockerfile

@@ -0,0 +1,40 @@
+FROM dceoy/r-tidyverse
+
+MAINTAINER Kiran V Garimella
+
+# install some utilities
+RUN apt-get update -m
+RUN apt-get install -y wget datamash bsdmainutils git-lfs bzip2 ca-certificates libglib2.0-0 libxext6 libsm6 libxrender1 git mercurial subversion
+
+# install conda
+RUN wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O /miniconda.sh \
+        && bash /miniconda.sh -b -p /miniconda
+ENV PATH=/miniconda/bin/:/miniconda/envs/metrics/bin/:/root/google-cloud-sdk/bin/:${PATH}
+
+# install conda packages
+COPY ./environment.yml /
+RUN conda env create -f /environment.yml && conda clean -a
+RUN echo "source activate metrics" > ~/.bashrc
+RUN activate metrics
+
+# install more R packages
+#RUN set -e \
+#    && clir update \
+#    && clir install --devt=cran vroom \
+#    && clir validate vroom
+
+# install gatk
+RUN git clone https://github.com/broadinstitute/gatk.git -b kvg_pbeap \
+    && cd gatk \
+    && ./gradlew \
+    && cp /gatk/build/libs/gatk-package-4.1.0.0-54-g47086b6-SNAPSHOT-local.jar /usr/local/bin/gatk.jar \
+    && cd .. \
+    && rm -rf /gatk
+
+# install picard
+RUN wget -O /picard.jar https://github.com/broadinstitute/picard/releases/download/2.22.1/picard.jar
+
+# remove the entry point that we inherited from the r-tidyverse docker
+ENTRYPOINT []
+WORKDIR /
+CMD ["/bin/bash"]

cromwell/docker/metrics/Makefile

@@ -0,0 +1,10 @@
+VERSION = 0.2.0
+TAG = quay.io/corticall/metrics:$(VERSION)
+
+all: build push
+
+build:
+	docker build -t $(TAG) .
+
+push:
+	docker push $(TAG)

cromwell/docker/metrics/environment.yml

@@ -0,0 +1,12 @@
+name: metrics
+channels:
+  - defaults
+  - conda-forge
+  - bioconda
+dependencies:
+  - samtools
+  - bedtools
+  - java-jdk
+  - joblib
+  - matplotlib
+  - quast