New upstream version 5.1.5

    machine: true

    environment:

      - GCLOUD: /opt/google-cloud-sdk/bin/gcloud

      - BOTO_CONFIG: /dev/null

    steps:

      - checkout

      - restore_cache:

.git

.eggs

images

misc

.snakemake*

.idea

.pytest*

.cache

.ipynb*

.ropeproject

.test*

# Change Log

# [5.1.5] - 2018-06-24

## Changed

- fixed missing version info in docker image.

- several minor fixes to EGA support.

# [5.1.4] - 2018-05-28

## Added

- Allow `category` to be set.

## Changed

- Various cosmetic changes to reports.

- Fixed encoding issues in reports.

# [5.1.3] - 2018-05-22

## Changed

- Fixed various bugs in job groups, shadow directive, singularity directive, and more.

# [5.1.2] - 2018-05-18

## Changed

- Fixed a bug in the report stylesheet.

# [5.1.0] - 2018-05-17

## Added

- A new framework for self-contained HTML reports, including results, statistics and topology information. In future releases this will be further extended.

- A new utility snakemake.utils.validate() which allows to validate config and pandas data frames using JSON schemas.

- Two new flags --cleanup-shadow and --cleanup-conda to clean up old unused conda and shadow data.

## Changed

- Benchmark repeats are now specified inside the workflow via a new flag repeat().

- Command line interface help has been refactored into groups for better readability.

# [5.0.0] - 2018-05-11

# Added

- Group jobs for reduced queuing and network overhead, in particular with short running jobs.

- Output files can be marked as pipes, such that producing and consuming job are executed simultaneously and interfomation is transferred directly without using disk.

- Command line flags to clean output files.

- Command line flag to list files in working directory that are not tracked by Snakemake.

# Changes

- Fix of --default-remote-prefix in case of input functions returning lists or dicts.

- Scheduler no longer prefers jobs with many downstream jobs.

# [4.8.1] - 2018-04-25

# Added

- Allow URLs for the conda directive.

MAINTAINER Johannes Köster <johannes.koester@tu-dortmund.de>

ENV SINGULARITY_VERSION=2.4.5

ADD . /tmp/repo

RUN install_packages wget bzip2 ca-certificates gnupg2 squashfs-tools

RUN wget -O- http://neuro.debian.net/lists/xenial.us-ca.full > /etc/apt/sources.list.d/neurodebian.sources.list

RUN wget -O- http://neuro.debian.net/_static/neuro.debian.net.asc | apt-key add -

RUN install_packages singularity-container

RUN wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh && \

    bash Miniconda3-latest-Linux-x86_64.sh -b -p /opt/conda && \

    rm Miniconda3-latest-Linux-x86_64.sh

WORKDIR /tmp/repo

ENV PATH /opt/conda/bin:${PATH}

ENV LANG C.UTF-8

ENV SHELL /bin/bash

RUN conda update -n base conda && conda env update --name root --file /tmp/repo/environment.yml && conda clean --all -y

RUN pip install /tmp/repo

RUN install_packages wget bzip2 ca-certificates gnupg2 squashfs-tools git && \

    wget -O- http://neuro.debian.net/lists/xenial.us-ca.full > /etc/apt/sources.list.d/neurodebian.sources.list && \

    wget -O- http://neuro.debian.net/_static/neuro.debian.net.asc | apt-key add - && \

    install_packages singularity-container && \

    wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh && \

    bash Miniconda3-latest-Linux-x86_64.sh -b -p /opt/conda && \

    rm Miniconda3-latest-Linux-x86_64.sh && \

    conda update -n base conda && conda env update --name root --file /tmp/repo/environment.yml && conda clean --all -y && \

    pip install .