New upstream version 1.0.9

.idea/

__pycache__

.coverage

.pytest_cache

  - df -h

  - export PATH=~/install/bcbio-vm/anaconda/bin:$PATH

  - conda install --yes nomkl

  - travis_wait 30 conda install --yes -c conda-forge -c bioconda bcbio-nextgen-vm bcbio-nextgen

  - travis_wait conda install --yes -c conda-forge -c bioconda cwltool toil rabix-bunny

  - conda install --yes -c conda-forge -c bioconda bcbio-nextgen

  - conda install --yes -c conda-forge -c bioconda bcbio-nextgen-vm

  - conda install --yes -c conda-forge -c bioconda cwltool toil rabix-bunny

  # Clean up space with external tools we don't need for tests

  - conda clean --yes --tarballs --index-cache

  - conda remove --yes --force qt

  # Update to latest bcbio-nextgen code within the container

  - bcbio_vm.py devel setup_install -i quay.io/bcbio/bcbio-vc

  # -- Standard bcbio variant tests

  - docker run -v `pwd`:`pwd` quay.io/bcbio/bcbio-vc bash -c "cd `pwd` && /usr/local/share/bcbio-nextgen/anaconda/bin/py.test tests/unit --cov=bcbio"

  - py.test tests/bcbio_vm -v -m docker_multicore

  - docker run -v `pwd`:`pwd` quay.io/bcbio/bcbio-vc bash -c "cd `pwd` && /usr/local/share/bcbio-nextgen/anaconda/bin/py.test -p no:cacheprovider tests/unit --cov=bcbio"

  - py.test -p no:cacheprovider tests/bcbio_vm -v -m docker_multicore

  # -- bcbio variant CWL tests

  - py.test tests/bcbio_vm -v -s -m cwl_docker_joint

  - py.test tests/bcbio_vm -v -s -m cwl_docker_somatic

  - py.test -p no:cacheprovider tests/bcbio_vm -v -s -m cwl_docker_joint

  - py.test -p no:cacheprovider tests/bcbio_vm -v -s -m cwl_docker_somatic

  # -- platform integration

  - sudo mkdir -p /etc/pki/tls/certs && sudo ln -s /etc/ssl/certs/ca-certificates.crt /etc/pki/tls/certs/ca-bundle.crt

  - py.test tests/bcbio_vm -v -s -m cwl_arvados

  - py.test -p no:cacheprovider tests/bcbio_vm -v -s -m cwl_arvados

  # -- Cleanup variant docker image

  - docker ps -a -q | xargs --no-run-if-empty docker rm

  - docker rmi -f quay.io/bcbio/bcbio-vc

  - docker images

  - df -h

  - bcbio_vm.py devel setup_install -i quay.io/bcbio/bcbio-rnaseq

  - py.test tests/bcbio_vm -v -s -m cwl_docker_rnaseq

  - py.test -p no:cacheprovider tests/bcbio_vm -v -s -m cwl_docker_rnaseq

  # -- Cleanup RNA-seq docker image

  - docker ps -a -q | xargs --no-run-if-empty docker rm

  - docker rmi -f quay.io/bcbio/bcbio-rnaseq

# bcbio-nextgen installation

    mkdir -p /tmp/bcbio-nextgen-install && cd /tmp/bcbio-nextgen-install && \

    wget --no-check-certificate \

      https://raw.github.com/chapmanb/bcbio-nextgen/master/scripts/bcbio_nextgen_install.py && \

      https://raw.github.com/bcbio/bcbio-nextgen/master/scripts/bcbio_nextgen_install.py && \

    python bcbio_nextgen_install.py /usr/local/share/bcbio-nextgen \

      --isolate --nodata -u development --tooldir=/usr/local && \

      --isolate --minimize-disk --nodata -u development && \

    git config --global url.https://github.com/.insteadOf git://github.com/ && \

    /usr/local/share/bcbio-nextgen/anaconda/bin/conda install -y nomkl && \

    /usr/local/share/bcbio-nextgen/anaconda/bin/bcbio_nextgen.py upgrade --isolate --tooldir=/usr/local --tools && \

# add user run script

    wget --no-check-certificate -O createsetuser \

      https://raw.github.com/chapmanb/bcbio-nextgen-vm/master/scripts/createsetuser && \

      https://raw.github.com/bcbio/bcbio-nextgen-vm/master/scripts/createsetuser && \

    chmod a+x createsetuser && mv createsetuser /sbin && \

# clean filesystem

## 1.0.9 (10 April 2018)

- Use smoove for lumpy variant calling and genotyping, replacing custom lumpyexpress

  implementation: [validation](https://github.com/bcbio/bcbio_validations/tree/master/NA24385_sv#smoove-validation)

- Generalize exclusion of regions during variant calling with new

  `exclude_regions` target. Includes previously available LCR and high depth

  regions, in addition to removal of polyX and alternative contigs.

- Normalize allele frequency calculation and filtering for Strelka2 and MuTect2.

  Thanks to Vlad Saveliev.

- CNVkit: enable specification of pre-built reference background cnn with

  `background: cnv_reference`.

- CNVkit: handle projects with mixed CNVkit and non-CNVkit usage. Thanks to Luca

  Beltrame.

- Improved Atropos trimming: better use of multicore parallelization in variant

  and RNA-seq pipelines.

- Add support for polyG and polyX trimming to variant calling for NovaSeq 3' end

  cleanup and generally avoiding low complexity reads.

- Structural variant: use SURVIVOR for validation comparisons.

- RNA-seq variant calling: use multiple cores for VarDict.

- Support miRge2.0 for alternative small RNA annotation. Users should

  install the tool manually until compatible with bioconda.

- Add bamCoverage to chip-seq pipeline to calculate bigwig files.

- GATK4: Correctly use GATK4 GatherVcfs when tools_off: [gatk4] specified for

  variant calling. Thanks to Luca Beltrame.

- variant: Default to `mark_duplicates: false` if alignment turned off

  (`aligner: false`).

- variant: Fix race condition when preparing BED files for coverage and

  sv_regions. Thanks to Tristan Lubinski.

- Fix `noalt_calling` to correctly avoid parallelizing on non-standard

  chromosomes without a variant regions file.

- Fix broken `kraken` command. Thanks to @choosehappy.

## 1.0.8 (5 February 2018)

- GATK4 is the new default GATK release used in bcbio when running HaplotypeCaller or

of sequencing analysis, providing researchers with more time to focus on the

downstream biology.

.. image:: https://travis-ci.org/chapmanb/bcbio-nextgen.png

    :target: https://travis-ci.org/chapmanb/bcbio-nextgen

.. image:: https://travis-ci.org/bcbio/bcbio-nextgen.png

    :target: https://travis-ci.org/bcbio/bcbio-nextgen

Features

--------

1. `Install`_ ``bcbio-nextgen`` with all tool dependencies and data files::

         wget https://raw.github.com/chapmanb/bcbio-nextgen/master/scripts/bcbio_nextgen_install.py

         wget https://raw.github.com/bcbio/bcbio-nextgen/master/scripts/bcbio_nextgen_install.py

         python bcbio_nextgen_install.py /usr/local/share/bcbio --tooldir=/usr/local \

           --genomes GRCh37 --aligners bwa --aligners bowtie2

         cd project1/work

         bcbio_nextgen.py ../config/project1.yaml -n 8

.. _system configuration file: https://github.com/chapmanb/bcbio-nextgen/blob/master/config/bcbio_system.yaml

.. _sample description file: https://github.com/chapmanb/bcbio-nextgen/blob/master/config/bcbio_sample.yaml

.. _system configuration file: https://github.com/bcbio/bcbio-nextgen/blob/master/config/bcbio_system.yaml

.. _sample description file: https://github.com/bcbio/bcbio-nextgen/blob/master/config/bcbio_sample.yaml

.. _Automatically create a processing description: https://bcbio-nextgen.readthedocs.org/en/latest/contents/configuration.html#automated-sample-configuration

.. _Install: https://bcbio-nextgen.readthedocs.org/en/latest/contents/installation.html#automated

.. _configuration options: https://bcbio-nextgen.readthedocs.org/en/latest/contents/configuration.html

and discussion on the `biovalidation mailing list`_.

.. _full documentation: https://bcbio-nextgen.readthedocs.org

.. _GitHub: https://github.com/chapmanb/bcbio-nextgen/issues

.. _GitHub: https://github.com/bcbio/bcbio-nextgen/issues

.. _biovalidation mailing list: https://groups.google.com/d/forum/biovalidation

Contributors