diff --git a/.boto b/.boto new file mode 100644 index 000000000..727ea11e0 --- /dev/null +++ b/.boto @@ -0,0 +1,3 @@ +[Boto] +debug = 0 +num_retries = 10 diff --git a/foreman/dockerfiles/Dockerfile.foreman b/foreman/dockerfiles/Dockerfile.foreman index 412515a31..d8e1f154c 100644 --- a/foreman/dockerfiles/Dockerfile.foreman +++ b/foreman/dockerfiles/Dockerfile.foreman @@ -17,6 +17,7 @@ WORKDIR /home/user RUN pip3 install --upgrade pip COPY config config +COPY .boto .boto COPY foreman/requirements.txt . diff --git a/infrastructure/nomad-configuration/client-instance-user-data.tpl.sh b/infrastructure/nomad-configuration/client-instance-user-data.tpl.sh index 9be97232e..338b84c00 100644 --- a/infrastructure/nomad-configuration/client-instance-user-data.tpl.sh +++ b/infrastructure/nomad-configuration/client-instance-user-data.tpl.sh @@ -17,7 +17,7 @@ export DEBIAN_FRONTEND=noninteractive apt-get update -y apt-get upgrade -y -apt-get install --yes nfs-common jq iotop dstat speedometer +apt-get install --yes nfs-common jq iotop dstat speedometer awscli docker.io ulimit -n 65536 diff --git a/workers/dockerfiles/Dockerfile.affymetrix b/workers/dockerfiles/Dockerfile.affymetrix index 3c3866b12..4cdb39bc2 100644 --- a/workers/dockerfiles/Dockerfile.affymetrix +++ b/workers/dockerfiles/Dockerfile.affymetrix @@ -51,6 +51,7 @@ RUN pip3 install setuptools --upgrade && \ rm -rf /root/.cache COPY config/ config/ +COPY .boto .boto COPY common/dist/data-refinery-common-* common/ diff --git a/workers/dockerfiles/Dockerfile.downloaders b/workers/dockerfiles/Dockerfile.downloaders index f42487317..218d820a3 100644 --- a/workers/dockerfiles/Dockerfile.downloaders +++ b/workers/dockerfiles/Dockerfile.downloaders @@ -52,6 +52,7 @@ RUN sh aspera-cli-3.7.7.608.927cce8-linux-64-release.sh USER root COPY config config +COPY .boto .boto COPY workers/data_refinery_workers/downloaders/requirements.txt . diff --git a/workers/dockerfiles/Dockerfile.illumina b/workers/dockerfiles/Dockerfile.illumina index 37a808c90..74124aa30 100644 --- a/workers/dockerfiles/Dockerfile.illumina +++ b/workers/dockerfiles/Dockerfile.illumina @@ -44,6 +44,7 @@ RUN Rscript illumina_dependencies.R RUN pip3 install --upgrade pip COPY config/ config/ +COPY .boto .boto COPY workers/data_refinery_workers/processors/requirements.txt . diff --git a/workers/dockerfiles/Dockerfile.no_op b/workers/dockerfiles/Dockerfile.no_op index d5be2337b..0f3645832 100644 --- a/workers/dockerfiles/Dockerfile.no_op +++ b/workers/dockerfiles/Dockerfile.no_op @@ -55,6 +55,7 @@ RUN pip3 install --upgrade pip RUN pip3 --no-cache-dir install -r requirements.txt COPY config/ config/ +COPY .boto .boto COPY common/dist/data-refinery-common-* common/ # Get the latest version from the dist directory. diff --git a/workers/dockerfiles/Dockerfile.salmon b/workers/dockerfiles/Dockerfile.salmon index ae482413a..343d675cc 100644 --- a/workers/dockerfiles/Dockerfile.salmon +++ b/workers/dockerfiles/Dockerfile.salmon @@ -64,6 +64,7 @@ RUN chmod +x ./FastQC/fastqc RUN rm -f fastqc_v0.11.7.zip COPY config/ config/ +COPY .boto .boto COPY workers/data_refinery_workers/processors/requirements.txt . diff --git a/workers/dockerfiles/Dockerfile.smasher b/workers/dockerfiles/Dockerfile.smasher index df64deec1..d982c48ca 100644 --- a/workers/dockerfiles/Dockerfile.smasher +++ b/workers/dockerfiles/Dockerfile.smasher @@ -46,6 +46,7 @@ RUN pip3 install numpy scipy matplotlib pandas==0.23.1 scikit-learn sympy nose r # End smasher-specific COPY config/ config/ +COPY .boto .boto COPY workers/data_refinery_workers/processors/requirements.txt . diff --git a/workers/dockerfiles/Dockerfile.transcriptome b/workers/dockerfiles/Dockerfile.transcriptome index 6547da660..ecef6ae81 100644 --- a/workers/dockerfiles/Dockerfile.transcriptome +++ b/workers/dockerfiles/Dockerfile.transcriptome @@ -59,6 +59,7 @@ RUN rm -r Salmon* RUN pip3 install --upgrade pip COPY config/ config/ +COPY .boto .boto COPY workers/data_refinery_workers/processors/requirements.txt .