Commit 4016ff05 authored by Steffen Möller's avatar Steffen Möller
Browse files

New upstream version 1.1.5

parent 7e68a1c2

.travis.yml

+7 −7
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@@ -14,25 +14,25 @@ before_install: 
  # Temporal fix for networking problem: https://github.com/travis-ci/travis-ci/issues/1484

  - echo "127.0.1.1 "`hostname` | sudo tee /etc/hosts

  # Get and install anaconda for custom Python installation

  - wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh

  - bash Miniconda2-latest-Linux-x86_64.sh -b -p ~/install/bcbio-vm/anaconda

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

  - bash Miniconda3-latest-Linux-x86_64.sh -b -p ~/install/bcbio-vm/anaconda



install:

  # Install bcbio-nextgen and bcbio-nextgen-vm

  - df -h

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

  - conda install --yes nomkl

  - 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 bcbio-nextgen python=3

  - conda install --yes -c conda-forge -c bioconda bcbio-nextgen-vm python=3

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

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

  - conda remove --yes --force qt

  - rm -rf ~/install/bcbio-vm/anaconda/pkgs/qt-*

  - du -sch ~/install/bcbio-vm/anaconda/pkgs/* | sort -h

  - df -h

  # Update to latest bcbio-nextgen code externally and within the container

  - rm -rf ~/install/bcbio-vm/anaconda/lib/python2.7/site-packages/bcbio

  - rm -rf ~/install/bcbio-vm/anaconda/lib/python2.7/site-packages/bcbio_nextgen-*

  # Update to latest bcbio-nextgen code externally

  - rm -rf ~/install/bcbio-vm/anaconda/lib/python*/site-packages/bcbio

  - rm -rf ~/install/bcbio-vm/anaconda/lib/python*/site-packages/bcbio_nextgen-*

  - ~/install/bcbio-vm/anaconda/bin/python setup.py install



jobs:

HISTORY.md

+15 −0
Original line number Diff line number Diff line 
## 1.1.5 (12 April 2019)



- Fixes for Python3 incompatibilities on distributed IPython runs.

- Numerous smaller Python3 incompatibilities with strings/unicode and types.

  Thanks to the community for reporting these.

- GATK HaplotypeCaller: correctly apply skipping of marked duplicates only

  for amplicon runs. Thanks to Ben Liesfeld.

- Fix format detection for bzip2 fastq inputs.

- Support latest GATK4 MuTect2 (4.1.1.0) with changes to ploidy and reference

  parameters.

- Support changes to GATK4 for VQSR --resource specification in 4.1.1.0. Thanks

  to Timothee Cezard.

- Support latest bedtools (2.28.0) which expects SAM heads for bgzipped BED

  inputs.



## 1.1.4 (3 April 2019)



- Move to Python 3.6. A python2 environment in the install runs non python3

bcbio/distributed/ipythontasks.py

+12 −1
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@@ -68,7 +68,18 @@ def _pack_n_log(f): 
            return ipython.zip_args(fn(*args))

    return wrapper



@require(sample)

def apply(object, args=None, kwargs=None):

    """Python3 apply replacement for double unpacking of inputs during apply.



    Thanks to: https://github.com/stefanholek/apply

    """

    if args is None:

        args = ()

    if kwargs is None:

        kwargs = {}

    return object(*args, **kwargs)



require(sample)

def prepare_sample(*args):

    args = ipython.unzip_args(args)

    with _setup_logging(args) as config:

bcbio/galaxy/nglims.py

+1 −2
Original line number Diff line number Diff line
@@ -4,7 +4,6 @@ from __future__ import print_function 
import collections

import copy

import glob

import gzip

import operator

import os

import subprocess
@@ -53,7 +52,7 @@ def _prep_sample_and_config(ldetail_group, fastq_dir, fastq_final_dir): 
            return out



def _non_empty(f):

    with gzip.open(f) as in_handle:

    with utils.open_gzipsafe(f) as in_handle:

        for line in in_handle:

            return True

    return False

bcbio/heterogeneity/loh.py

+1 −2
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@@ -4,7 +4,6 @@ Provides high level summaries of calls in regions of interest. 
"""

import csv

import collections

import gzip

import os

import decimal

import uuid
@@ -61,7 +60,7 @@ def _civic_regions(civic_file, variant_types=None, diseases=None, drugs=None): 
    """

    if isinstance(diseases, six.string_types):

        diseases = [diseases]

    with gzip.open(civic_file) as in_handle:

    with utils.open_gzipsafe(civic_file) as in_handle:

        reader = csv.reader(in_handle, delimiter="\t")

        for chrom, start, end, info_str in reader:

            info = edn_loads(info_str)