From d3f0ae852ddabef9e755ff0565faf7f855f2e211 Mon Sep 17 00:00:00 2001 From: Darryl Nousome Date: Thu, 30 May 2024 11:42:25 -0400 Subject: [PATCH 1/2] revert: lofreq separate docker --- docker/lofreq/Dockerfile | 59 ++++++++++++++++++++++++++++++++++++ docker/lofreq/build.sh | 5 +++ docker/lofreq/meta.yml | 4 +++ docker/logan_base/Dockerfile | 21 +++++++------ 4 files changed, 79 insertions(+), 10 deletions(-) create mode 100644 docker/lofreq/Dockerfile create mode 100644 docker/lofreq/build.sh create mode 100644 docker/lofreq/meta.yml diff --git a/docker/lofreq/Dockerfile b/docker/lofreq/Dockerfile new file mode 100644 index 0000000..15e56f5 --- /dev/null +++ b/docker/lofreq/Dockerfile @@ -0,0 +1,59 @@ +FROM --platform=linux/amd64 ubuntu:22.04 + +# build time variables +ARG BUILD_DATE="000000" +ENV BUILD_DATE=${BUILD_DATE} +ARG BUILD_TAG="000000" +ENV BUILD_TAG=${BUILD_TAG} +ARG REPONAME="000000" +ENV REPONAME=${REPONAME} + +LABEL maintainer + +# Create Container filesystem specific +# working directory and opt directories + +# This section installs system packages required for your project +# If you need extra system packages add them here. +RUN apt-get update \ + && apt-get -y upgrade \ + && DEBIAN_FRONTEND=noninteractive apt-get install -y \ + automake \ + build-essential \ + curl \ + git \ + gcc \ + libbz2-dev \ + libcurl4-gnutls-dev \ + libgsl0-dev \ + libperl-dev \ + liblzma-dev \ + libncurses5-dev \ + libssl-dev \ + python3-dev \ + zlib1g-dev + +RUN ln -s /usr/bin/python3.10 /usr/bin/python + +WORKDIR /opt2 + +ARG htsversion=1.19 + +RUN curl -L https://github.com/samtools/htslib/releases/download/${htsversion}/htslib-${htsversion}.tar.bz2 | tar xj \ + && cd htslib-${htsversion} \ + && ./configure \ + && make \ + && make install + +RUN curl -L https://github.com/samtools/bcftools/releases/download/${htsversion}/bcftools-${htsversion}.tar.bz2 | tar xj \ + && cd bcftools-${htsversion} \ + && ./configure && make && make install + +RUN git clone https://github.com/CSB5/lofreq \ + && cd lofreq \ + && ./bootstrap \ + && ./configure --with-htslib=/usr/local \ + && make \ + && make install + +ENV LD_LIBRARY_PATH /usr/local/lib:$LD_LIBRARY_PATH \ No newline at end of file diff --git a/docker/lofreq/build.sh b/docker/lofreq/build.sh new file mode 100644 index 0000000..9df32f9 --- /dev/null +++ b/docker/lofreq/build.sh @@ -0,0 +1,5 @@ +docker build --platform linux/amd64 --tag ccbr_lofreq:v0.0.1 -f Dockerfile . + +docker tag ccbr_lofreq:v0.0.1 dnousome/ccbr_lofreq:v0.0.1 +docker push dnousome/ccbr_lofreq:v0.0.1 +docker push dnousome/ccbr_lofreq:latest \ No newline at end of file diff --git a/docker/lofreq/meta.yml b/docker/lofreq/meta.yml new file mode 100644 index 0000000..7138be5 --- /dev/null +++ b/docker/lofreq/meta.yml @@ -0,0 +1,4 @@ +dockerhub_namespace: dnousome +image_name: ccbr_lofreq +version: v0.0.1 +container: "$(dockerhub_namespace)/$(image_name):$(version)" diff --git a/docker/logan_base/Dockerfile b/docker/logan_base/Dockerfile index b60fadc..58220ae 100644 --- a/docker/logan_base/Dockerfile +++ b/docker/logan_base/Dockerfile @@ -46,17 +46,18 @@ RUN wget https://github.com/biod/sambamba/releases/download/v0.8.1/sambamba-0.8. && mv /opt2/sambamba-0.8.1-linux-amd64-static /opt2/sambamba \ && chmod a+rx /opt2/sambamba -# Install GATK4 (GATK/4.4.0.0) +# Install GATK4 (GATK/4.5.0.0) # Requires Java17 -RUN wget https://github.com/broadinstitute/gatk/releases/download/4.4.0.0/gatk-4.4.0.0.zip \ - && unzip /opt2/gatk-4.4.0.0.zip \ - && rm /opt2/gatk-4.4.0.0.zip \ - && /opt2/gatk-4.4.0.0/gatk --list -ENV PATH="/opt2/gatk-4.4.0.0:$PATH" - -# Use DISCVRSeq For CombineVariants Replacement -RUN wget https://github.com/BimberLab/DISCVRSeq/releases/download/1.3.62/DISCVRSeq-1.3.62.jar -ENV DISCVRSeq_JAR="/opt2/DISCVRSeq-1.3.62.jar" +RUN wget https://github.com/broadinstitute/gatk/releases/download/4.5.0.0/gatk-4.5.0.0.zip \ + && unzip /opt2/gatk-4.5.0.0.zip \ + && rm /opt2/gatk-4.5.0.0.zip \ + && /opt2/gatk-4.5.0.0/gatk --list +ENV PATH="/opt2/gatk-4.5.0.0:$PATH" + + +#Use DISCVRSeq For CombineVariants Replacement +#RUN wget https://github.com/BimberLab/DISCVRSeq/releases/download/1.3.62/DISCVRSeq-1.3.62.jar +#ENV DISCVRSeq_JAR="/opt2/DISCVRSeq-1.3.62.jar" # Install last release of GATK3 (GATK/3.8-1) # Only being used for the CombineVariants From 00339182f820cd54ee8e9ea6817c28806352e2d4 Mon Sep 17 00:00:00 2001 From: Darryl Nousome Date: Thu, 30 May 2024 11:44:57 -0400 Subject: [PATCH 2/2] revert: lofreq! --- conf/containers.config | 2 +- docker/logan_base/Dockerfile | 10 ---------- modules/local/variant_calling.nf | 3 +-- 3 files changed, 2 insertions(+), 13 deletions(-) diff --git a/conf/containers.config b/conf/containers.config index a167cf7..385c9c2 100644 --- a/conf/containers.config +++ b/conf/containers.config @@ -2,7 +2,7 @@ params { containers { base = 'docker://nciccbr/ccbr_ubuntu_base_20.04:v6.1' - logan = 'docker://dnousome/ccbr_logan_base:v0.3.4' + logan = 'docker://dnousome/ccbr_logan_base:v0.3.5' vcf2maf = 'docker://dnousome/ccbr_vcf2maf:v102.0.0' lofreq = 'docker://dnousome/ccbr_lofreq:v0.0.1' octopus = 'docker://dancooke/octopus:latest' diff --git a/docker/logan_base/Dockerfile b/docker/logan_base/Dockerfile index 58220ae..7da9e7b 100644 --- a/docker/logan_base/Dockerfile +++ b/docker/logan_base/Dockerfile @@ -192,16 +192,6 @@ RUN wget -O svaba_1.2.0 https://github.com/walaj/svaba/releases/download/v1.2.0/ ENV PATH="/opt2/svaba:$PATH" -# LOFREQ -RUN git clone https://github.com/CSB5/lofreq \ - && cd /opt2/lofreq \ - && ./bootstrap \ - && ./configure --prefix=/opt2/lofreq/ \ - && make \ - && make install - -ENV PATH="/opt2/lofreq/bin:$PATH" - # MUSE RUN wget -O muse_2.0.4.tar.gz https://github.com/wwylab/MuSE/archive/refs/tags/v2.0.4.tar.gz \ && tar -xzf muse_2.0.4.tar.gz \ diff --git a/modules/local/variant_calling.nf b/modules/local/variant_calling.nf index f51d546..c1cab84 100644 --- a/modules/local/variant_calling.nf +++ b/modules/local/variant_calling.nf @@ -520,7 +520,7 @@ script: process lofreq_tn { - container "${params.containers.logan}" + container "${params.containers.lofreq}" label 'process_somaticcaller' input: @@ -529,7 +529,6 @@ process lofreq_tn { output: - tuple val(tumorname), val(normalname), path("${tumorname}_vs_${normalname}_${bed.simpleName}_somatic_final.snvs.vcf.gz"), path("${tumorname}_vs_${normalname}_${bed.simpleName}_somatic_final_minus-dbsnp.snvs.vcf.gz"),