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#

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

#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

#

#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

#
#
#

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
#

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

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sauloal
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