Merge pull request #50 from CCBR/fix_docker

revert: lofreq separate docker
CCBR · May 30, 2024 · c7d8879 · c7d8879
2 parents ea50c67 + 0033918
commit c7d8879
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Showing 6 changed files with 80 additions and 22 deletions.
diff --git 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/lofreq/Dockerfile 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=${REPONAME}
+
+LABEL maintainer <[email protected]>
+
+# Create Container filesystem specific 
+# working directory and opt directories 
+
+# This section installs system packages required for your project
+# If you need extra system packages add them here.
+RUN apt-get update \
+ && apt-get -y upgrade \
+ && DEBIAN_FRONTEND=noninteractive apt-get install -y \
+      automake \
+      build-essential \
+	curl \
+      git \
+      gcc \
+	libbz2-dev \
+	libcurl4-gnutls-dev \
+	libgsl0-dev \
+    	libperl-dev \
+	liblzma-dev \
+	libncurses5-dev \
+	libssl-dev \
+      python3-dev \
+	zlib1g-dev 
+
+RUN ln -s /usr/bin/python3.10 /usr/bin/python
+
+WORKDIR /opt2 
+
+ARG htsversion=1.19
+
+RUN curl -L https://github.com/samtools/htslib/releases/download/${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
diff --git a/docker/lofreq/build.sh 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
diff --git a/docker/lofreq/meta.yml 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
@@ -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:$PATH"
+RUN wget https://github.com/broadinstitute/gatk/releases/download/4.5.0.0/gatk-4.5.0.0.zip \
+    && unzip /opt2/gatk-4.5.0.0.zip \
+    && rm /opt2/gatk-4.5.0.0.zip \
+    && /opt2/gatk-4.5.0.0/gatk --list
+ENV PATH="/opt2/gatk-4.5.0.0:$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"
+
+#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
@@ -191,16 +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
@@ -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"),