I am created a docker container with hisat_genotype -- so when I run the program with the example HLA data (ILMN.tar.gz NA12877) -- looks like the program downloads the grch38.tar.gz file -- which was downloaded during the installation.
Despite getting the following errors -- the additional time in getting the file and creating the index for hisat2 (despite it being present in the indices directory) makes the program quite slow...
gzip: stdin: unexpected end of file
tar: Child returned status 1
tar: Error is not recoverable: exiting now
mv: inter-device move failed: 'grch38' to '/usr/local/hisat-genotype/indicies/grch38'; unable to remove target: Directory not empty
Here is my Dockerfile contents
FROM google/cloud-sdk:slim
ENV SAMTOOLS_VER="1.13"
RUN apt-get update; apt-get install -y build-essential checkinstall; apt-get upgrade; \
DEBIAN_FRONTEND="noninteractive" apt-get install -y --allow-unauthenticated libreadline-gplv2-dev libncursesw5-dev libssl-dev libsqlite3-dev tk-dev libgdbm-dev libc6-dev libbz2-dev zlib1g-dev liblzma-dev libcurl4-gnutls-dev libncurses5-dev wget unzip git default-jre default-jdk r-base cpanminus pigz parallel python3
RUN cd /opt; wget https://github.com/samtools/samtools/releases/download/${SAMTOOLS_VER}/samtools-${SAMTOOLS_VER}.tar.bz2; \
tar -vxjf samtools-${SAMTOOLS_VER}.tar.bz2; rm samtools-${SAMTOOLS_VER}.tar.bz2; \
cd samtools-${SAMTOOLS_VER}; \
./configure; make; make install;
RUN cd /opt; wget https://github.com/samtools/htslib/releases/download/${SAMTOOLS_VER}/htslib-${SAMTOOLS_VER}.tar.bz2; \
tar -vxjf htslib-${SAMTOOLS_VER}.tar.bz2; rm htslib-${SAMTOOLS_VER}.tar.bz2; \
cd htslib-${SAMTOOLS_VER}; \
./configure; make; make install;
RUN cd /opt; wget https://github.com/samtools/bcftools/releases/download/${SAMTOOLS_VER}/bcftools-${SAMTOOLS_VER}.tar.bz2; \
tar -vxjf bcftools-${SAMTOOLS_VER}.tar.bz2; rm bcftools-${SAMTOOLS_VER}.tar.bz2; \
cd bcftools-${SAMTOOLS_VER}; \
./configure; make; make install;
#RUN /usr/local; wget https://github.com/DaehwanKimLab/hisat-genotype/archive/refs/tags/v1.3.3.tar.gz; tar xvfz v1.3.3.tar.gz; mv hisat-genotype-1.3.3 hisat-genotype; cd hisat-genotype; git clone https://github.com/DaehwanKimLab/hisat2.git; cd hisat2; make; cd ..; bash setup.sh -r
RUN cd /usr/local; git clone https://github.com/DaehwanKimLab/hisat-genotype.git; cd hisat-genotype; bash setup.sh -r
ENV PYTHONPATH "$PYTHONPATH:/usr/local/hisat-genotype/hisatgenotype_modules"
ENV PATH "$PATH:/usr/local/bin:/usr/local/hisat-genotype:/usr/local/hisat-genotype/hisat2"
RUN ln -s /usr/bin/python3 /usr/bin/python
I am created a docker container with hisat_genotype -- so when I run the program with the example HLA data (ILMN.tar.gz NA12877) -- looks like the program downloads the grch38.tar.gz file -- which was downloaded during the installation.
Despite getting the following errors -- the additional time in getting the file and creating the index for hisat2 (despite it being present in the indices directory) makes the program quite slow...
gzip: stdin: unexpected end of file tar: Child returned status 1 tar: Error is not recoverable: exiting now mv: inter-device move failed: 'grch38' to '/usr/local/hisat-genotype/indicies/grch38'; unable to remove target: Directory not empty Here is my Dockerfile contents