sauloal/masurca repository overview

#TO BUILD: docker build -t sauloal/masurca .

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#TO RUN MANUALLY :

⁠FROM INSIDE THE FOLDER CONTAINING THE MOUSE DATA, RUN:

⁠chmod o+w .

⁠docker run --rm -it --name masurca_mouse -v $PWD:/data:rw sauloal/masurca bash

⁠masurca mm_config.cfg

⁠./assembly.sh

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#TO RUN AUTOMATICALLY:

⁠FROM INSIDE THE FOLDER CONTAINING THE MOUSE DATA, RUN:

⁠chmod o+w .

⁠docker run --rm -it --name masurca_mouse -v $PWD:/data:rw sauloal/masurca masurca mm_config.cfg

⁠docker run --rm -it --name masurca_mouse -v $PWD:/data:rw sauloal/masurca ./assembly.sh

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⁠example configuration file

⁠mm_config.cfg

#DATA #PE= pe 180 20 /data/pe_1.fastq /data/pe_2.fastq #JUMP= j1 1834 182 /data/sj_1834_182_1.fastq /data/sj_1834_182_2.fastq #JUMP= j2 2289 2794 /data/sj_2289_212_1.fastq /data/sj_2289_212_2.fastq #JUMP= j3 2794 220 /data/sj_2794_220_1.fastq /data/sj_2794_220_2.fastq #JUMP= j4 -38453 3557 /data/lj_38453_3557_2.fastq /data/lj_38453_3557_1.fastq #END #GRAPH_KMER_SIZE=auto #USE_LINKING_MATES=0 #LIMIT_JUMP_COVERAGE = 60 #CA_PARAMETERS = ovlMerSize=30 cgwErrorRate=0.10 ovlMemory=40GB #KMER_COUNT_THRESHOLD = 1 #NUM_THREADS= 20 #JF_SIZE=10000000000 #DO_HOMOPOLYMER_TRIM=0 #END

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FROM ubuntu:14.04

ENV DEBIAN_FRONTEND noninteractive ENV DEBIAN_PRIORITY critical ENV DEBCONF_NOWARNINGS yes

RUN apt-get update RUN apt-get install -y build-essential wget python python-dev bzip2 libbz2-dev gawk;
apt-get clean all

RUN wget ftp://ftp.genome.umd.edu/pub/MaSuRCA/v2.2.1/MaSuRCA-2.2.1.tar.gz &&
tar xvf MaSuRCA-2.2.1.tar.gz &&
cd MaSuRCA-2.2.1 &&
./install.sh

ENV LD_LIBRARY_PATH /MaSuRCA-2.2.1/lib

ENV PATH $PATH:/MaSuRCA-2.2.1/bin

WORKDIR /data