New upstream version 4.8.1

SINGULARITY_VER=2.4.2

SINGULARITY_VER=2.4.5

*.egg

.eggs/

.snakemake*

.idea

# Change Log

# [4.8.1] - 2018-04-25

# Added

- Allow URLs for the conda directive.

# Changed

- Various minor updates in the docs.

- Several bug fixes with remote file handling.

- Fix ImportError occuring with script directive.

- Use latest singularity.

- Improved caching for file existence checks. We first check existence of parent directories and cache these results. By this, large parts of the generated FS tree can be pruned if files are not yet present. If files are present, the overhead is minimal, since the checks for the parents are cached.

- Various minor bug fixes.

# [4.8.0] - 2018-03-13

### Added

- Integration with CWL: the `cwl` directive allows to use CWL tool definitions in addition to shell commands or Snakemake wrappers.

### Added

- A new shadow mode (minimal) that only symlinks input files has been added.

### Changed

- The default shell is now bash on linux and maxOS. If bash is not installed, we fall back to sh. Previously, Snakemake used the default shell of the user, which defeats the purpose of portability. If the developer decides so, the shell can be always overwritten using shell.executable().

- The default shell is now bash on linux and macOS. If bash is not installed, we fall back to sh. Previously, Snakemake used the default shell of the user, which defeats the purpose of portability. If the developer decides so, the shell can be always overwritten using shell.executable().

- Snakemake now requires Singularity 2.4.1 at least (only when running with --use-singularity).

- HTTP remote provider no longer automatically unpacks gzipped files.

- Fixed various smaller bugs.

### Changed

- The scheduler now tries to get rid of the largest temp files first.

- The Docker image used for kubernetes support can now be configured at the command line.

- Rate-limiting for cluster interaction has be unified.

- Rate-limiting for cluster interaction has been unified.

- S3 remote provider uses boto3.

- Resource functions can now use an additional `attempt` parameter, that contains the number of times this job has already been tried.

- Various minor fixes.

### Changed

- Benchmark files now also include the maximal RSS and VMS size of the Snakemake process and all sub processes.

- Speedup conda environment creation.

- Allow specification, of DRMAA log dir.

- Allow specification of DRMAA log dir.

- Pass cluster config to subworkflow.

## [3.9.0] - 2016-11-15

### Added

- Ability to define isolated conda software environments (YAML) per rule. Environment will be deployed by Snakemake upon workflow execution.

- Ability to define isolated conda software environments (YAML) per rule. Environments will be deployed by Snakemake upon workflow execution.

- Command line argument --wrapper-prefix in order to overwrite the default URL for looking up wrapper scripts.

### Changed

- --summary now displays the log files correspoding to each output file.

FROM bitnami/minideb:stretch

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

ENV SINGULARITY_VERSION=2.3.2

ENV SINGULARITY_VERSION=2.4.5

ADD . /tmp/repo

RUN install_packages wget bzip2 ca-certificates gnupg2

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

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

ENV LANG C.UTF-8

ENV SHELL /bin/bash

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

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

.. code-block:: console

    $ conda install -c bioconda snakemake

    $ conda install -c bioconda -c conda-forge snakemake

from the `Bioconda <https://bioconda.github.io>`_ channel.