New upstream version 5.6.0

SINGULARITY_VER=2.5.1

SINGULARITY_VER=3.3.0

            # TODO only install if singularity is not yet present

            # if type singularity > /dev/null; then exit 0; fi

            source .circleci/common.sh

            sudo apt-get update; sudo apt-get install squashfs-tools libarchive-dev

            wget https://github.com/singularityware/singularity/releases/download/$SINGULARITY_VER/singularity-$SINGULARITY_VER.tar.gz

            tar xvf singularity-$SINGULARITY_VER.tar.gz

            cd singularity-$SINGULARITY_VER

            ./configure --prefix=/usr/local --sysconfdir=/etc

            make

            sudo make install

            sudo add-apt-repository ppa:gophers/archive

            sudo apt-get update

            sudo apt-get install build-essential libssl-dev uuid-dev libgpgme11-dev libseccomp-dev wget pkg-config squashfs-tools libarchive-dev golang-1.11

            export PATH=/usr/lib/go-1.11/bin:$PATH

            wget https://github.com/sylabs/singularity/releases/download/v${SINGULARITY_VER}/singularity-${SINGULARITY_VER}.tar.gz

            tar -xvf singularity-$SINGULARITY_VER.tar.gz

            cd singularity

            ./mconfig

            make -C builddir

            sudo make -C builddir install

      - run:

          name: Setup Snakemake

          command: |

.ipynb*

.ropeproject

.test*

tests/test*/*

playground/*

tutorial/*

 No newline at end of file

[5.6.0] - 2019-09-06

====================

Changed

-------

- Fix compatibility with latest singularity versions.

- Various bug fixes (e.g. in cluster error handling, remote providers, kubernetes backend).

Added

-----

- Add --default-resources flag, that allows to define default resources for jobs (e.g. mem_mb, disk_mb), see `docs <https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#resources>`_.

- Accept ``--dry-run`` as a synonym of ``--dryrun``. Other Snakemake options are similarly hyphenated, so other documentation now refers to ``--dry-run`` but both (and also ``-n``) will always be accepted equivalently.

[5.5.4] - 2019-07-21

====================

Changed

    $ snakemake --cluster "qsub {threads}"

Thereby, all keywords of a rule are allowed (e.g. params, input, output, threads, priority, ...).

Thereby, all keywords of a rule are allowed (e.g. rulename, params, input, output, threads, priority, ...).

For example, you could encode the expected running time into params:

.. code-block:: python

Job Properties

~~~~~~~~~~~~~~

When executing a workflow on a cluster using the ``--cluster`` parameter (see below), Snakemake creates a job script for each job to execute. This script is then invoked using the provided cluster submission command (e.g. ``qsub``). Sometimes you want to provide a custom wrapper for the cluster submission command that decides about additional parameters. As this might be based on properties of the job, Snakemake stores the job properties (e.g. rule name, threads, input files, params etc.) as JSON inside the job script. For convenience, there exists a parser function `snakemake.utils.read_job_properties` that can be used to access the properties. The following shows an example job submission wrapper:

When executing a workflow on a cluster using the ``--cluster`` parameter (see below), Snakemake creates a job script for each job to execute. This script is then invoked using the provided cluster submission command (e.g. ``qsub``). Sometimes you want to provide a custom wrapper for the cluster submission command that decides about additional parameters. As this might be based on properties of the job, Snakemake stores the job properties (e.g. name, rulename, threads, input, output, params etc.) as JSON inside the job script (for group jobs, the rulename will be "GROUP", otherwise it will be the same as the job name). For convenience, there exists a parser function `snakemake.utils.read_job_properties` that can be used to access the properties. The following shows an example job submission wrapper:

.. code-block:: python

    os.system("qsub -t {threads} {script}".format(threads=threads, script=jobscript))

.. _profiles:

--------

Profiles

--------