New upstream version 0.3.1

*.pyc

.*.swp

build/

dist/

pbalign.egg-info/

.DS_Store

include LICENSES.txt

develop:

	python setup.py develop

test:

pylint:

	pylint --errors-only pbalign

test: pylint

	# Unit tests

	#find tests/unit -name "*.py" | xargs nosetests

	nosetests --verbose tests/unit/*.py

	python setup.py test

	# End-to-end tests

	@echo pbalign cram tests require blasr installed.

	find tests/cram -name "*.t" | xargs cram 

Want to know how to install and run pbalign?

Please refer to https://github.com/PacificBiosciences/pbalign/blob/master/doc/howto.rst

DISCLAIMER

----------

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#!/usr/bin/env bash

set -vex

################

# DEPENDENCIES #

################

## Load modules

type module >& /dev/null || . /mnt/software/Modules/current/init/bash

module purge

module load gcc

module load git

module load samtools

module load python/2

case "${bamboo_planRepository_branchName}" in

  master)

    module load blasr/master

    ;;

  *)

    module load blasr/develop

    ;;

esac

rm -rf prebuilts build

test -d .pip/wheels && find .pip/wheels -type f ! -name '*none-any.whl' -print -delete || true

export NX3PBASEURL=http://nexus/repository/unsupported/pitchfork/gcc-6.4.0

export PATH="${PWD}/build/bin:${PATH}"

export PYTHONUSERBASE="${PWD}/build"

export PIP="pip --cache-dir=$bamboo_build_working_directory/.pip"

CUR_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"

source "${CUR_DIR}"/scripts/ci/build.sh

source "${CUR_DIR}"/scripts/ci/test.sh