STAR-Fusion container 0.0.1

star-fusion/Dockerfile

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+# STAR-Fusion Dockerfile 
+# https://github.com/STAR-Fusion/STAR-Fusion/wiki
+
+FROM ubuntu:16.04
+
+MAINTAINER Jacob Pfeil, [email protected]
+
+RUN apt-get update --fix-missing && \
+    apt-get install -y python zlib1g-dev gzip perl libdb-dev \
+                       build-essential wget make git
+
+# Install perl libraries 
+RUN cpan App::cpanminus && cpanm Set::IntervalTree && cpanm DB_File && cpanm URI 
+
+WORKDIR /home
+
+# Need STAR binary
+RUN wget https://github.com/alexdobin/STAR/archive/2.5.2b.tar.gz && \
+    tar -xzf 2.5.2b.tar.gz && \
+    git clone --recursive https://github.com/STAR-Fusion/STAR-Fusion.git
+
+# Add STAR and STAR-Fusion to path
+ENV PATH "/home/STAR-2.5.2b/bin/Linux_x86_64/:/home/STAR-Fusion/:$PATH"
+
+# Add wrapper scripts 
+ADD star_fusion_wrapper.sh /home/star_fusion_wrapper.sh
+ADD star_fusion_pipeline.py /home/star_fusion_pipeline.py
+ADD genelist.txt /home/genelist.txt
+
+# Data processing occurs at /data
+WORKDIR /data
+
+ENTRYPOINT ["sh", "/home/star_fusion_wrapper.sh"]
+CMD ["-h"]

star-fusion/README.md

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+
+STAR-Fusion for Treehouse RNA-seq analysis
+====================
+
+
+### Overview
+
+Gene fusions play a major role in tumorigenesis, so it is crucial that Treehouse has a pipeline for detecting them. We have built a docker container that runs [STAR-Fusion](https://github.com/STAR-Fusion/STAR-Fusion/wiki) and filters the output against a list of known cancer fusion genes. 
+
+### Docker and usage
+
+##### Image located on hub.docker.com
+
+REPOSITORY: jpfeil/star-fusion
+
+TAG: 0.0.1
+
+IMAGE ID: 520e7a15847b
+
+
+##### Input files
+
+The pipeline requires paired-end fastq files, the output directory, and the genome library directory. The genelist is already baked into the docker container, but there is an option to include a different genelist. Please refer to the STAR-Fusion documentation for creating a genome library. You can also find a prebuilt genome library here: `http://ceph-gw-01.pod/references/STARFusion-GRCh38gencode23.tar.gz` 
+
+```
+usage: star_fusion_pipeline.py [-h] --left_fq R1 --right_fq R2 --output_dir
+                               OUTPUT_DIR --genome_lib_dir GENOME_LIB_DIR
+                               [--CPU CPU] [--genelist GENELIST]
+                               [--skip_filter] [--test]
+
+Wraps STAR-Fusion program and filters output.
+
+optional arguments:
+  -h, --help            show this help message and exit
+  --left_fq R1          Fastq 1
+  --right_fq R2         Fastq 2
+  --output_dir OUTPUT_DIR
+                        Output directory
+  --genome_lib_dir GENOME_LIB_DIR
+                        Genome library directory
+  --CPU CPU             Number of cores
+  --genelist GENELIST
+  --skip_filter
+  --test
+
+```
+
+
+##### Run command
+```
+docker run -it --rm -v `pwd`:/data jpfeil/star-fusion:0.0.1 \
+                                   --left_fq 1.fq.gz \
+                                   --right_fq 2.fq.gz \
+                                   --output_dir fusion_output \
+                                   --CPU `nproc` \
+                                   --genome_lib_dir STARFusion-GRCh38gencode23
+```
+
+### **Output**
+
+There will be many files in the output directory, but you can find the fusion calls in these files:
+
+- `star-fusion.fusion_candidates.final.abridged`
+- `star-fusion.fusion_candidates.final.in_genelist.abridged`
+
+The second file contains fusion calls were both fusion partners are in the genelist.