galaxy/scripts/common_startup.sh

#!/bin/bash
set -e

GXPIP_VERSION='8.0.2+gx2'

SET_VENV=1
for arg in "$@"; do
    [ "$arg" = "--skip-venv" ] && SET_VENV=0
done

# Conda Python is in use, do not use virtualenv
if python -V 2>&1 | grep -q 'Continuum Analytics'; then
    SET_VENV=0
fi

DEV_WHEELS=0
FETCH_WHEELS=1
CREATE_VENV=1
REPLACE_PIP=$SET_VENV
COPY_SAMPLE_FILES=1

for arg in "$@"; do
    [ "$arg" = "--skip-eggs" ] && FETCH_WHEELS=0
    [ "$arg" = "--skip-wheels" ] && FETCH_WHEELS=0
    [ "$arg" = "--dev-wheels" ] && DEV_WHEELS=1
    [ "$arg" = "--no-create-venv" ] && CREATE_VENV=0
    [ "$arg" = "--no-replace-pip" ] && REPLACE_PIP=0
    [ "$arg" = "--replace-pip" ] && REPLACE_PIP=1
    [ "$arg" = "--stop-daemon" ] && FETCH_WHEELS=0
    [ "$arg" = "--skip-samples" ] && COPY_SAMPLE_FILES=0
done

SAMPLES="
    config/migrated_tools_conf.xml.sample
    config/shed_tool_conf.xml.sample
    config/shed_tool_data_table_conf.xml.sample
    config/shed_data_manager_conf.xml.sample
    lib/tool_shed/scripts/bootstrap_tool_shed/user_info.xml.sample
    tool-data/shared/ucsc/builds.txt.sample
    tool-data/shared/ucsc/manual_builds.txt.sample
    tool-data/shared/ucsc/ucsc_build_sites.txt.sample
    tool-data/shared/igv/igv_build_sites.txt.sample
    tool-data/shared/rviewer/rviewer_build_sites.txt.sample
    tool-data/*.sample
    static/welcome.html.sample
"

RMFILES="
    lib/pkg_resources.pyc
"

if [ $COPY_SAMPLE_FILES -eq 1 ]; then
	# Create any missing config/location files
	for sample in $SAMPLES; do
		file=${sample%.sample}
	    if [ ! -f "$file" -a -f "$sample" ]; then
	        echo "Initializing $file from `basename $sample`"
	        cp $sample $file
	    fi
	done
fi

# remove problematic cached files
for rmfile in $RMFILES; do
    [ -f $rmfile ] && rm -f $rmfile
done

: ${GALAXY_CONFIG_FILE:=config/galaxy.ini}
if [ ! -f $GALAXY_CONFIG_FILE ]; then
    GALAXY_CONFIG_FILE=universe_wsgi.ini
fi
if [ ! -f $GALAXY_CONFIG_FILE ]; then
    GALAXY_CONFIG_FILE=config/galaxy.ini.sample
fi

: ${GALAXY_VIRTUAL_ENV:=.venv}

if [ $SET_VENV -eq 1 -a $CREATE_VENV -eq 1 ]; then
    # If .venv does not exist, attempt to create it.
    if [ ! -d "$GALAXY_VIRTUAL_ENV" ]
    then
        # Ensure Python is a supported version before creating .venv
        python ./scripts/check_python.py || exit 1
        if command -v virtualenv >/dev/null; then
            virtualenv "$GALAXY_VIRTUAL_ENV"
        else
            vvers=13.1.2
            vurl="https://pypi.python.org/packages/source/v/virtualenv/virtualenv-${vvers}.tar.gz"
            vsha="aabc8ef18cddbd8a2a9c7f92bc43e2fea54b1147330d65db920ef3ce9812e3dc"
            vtmp=`mktemp -d -t galaxy-virtualenv-XXXXXX`
            vsrc="$vtmp/`basename $vurl`"
            # SSL certificates are not checked to prevent problems with messed
            # up client cert environments. We verify the download using a known
            # good sha256 sum instead.
            echo "Fetching $vurl"
            if command -v curl >/dev/null; then
                curl --insecure -L -o $vsrc $vurl
            elif command -v wget >/dev/null; then
                wget --no-check-certificate -O $vsrc $vurl
            else
                python -c "import urllib; urllib.urlretrieve('$vurl', '$vsrc')"
            fi
            echo "Verifying $vsrc checksum is $vsha"
            python -c "import hashlib; assert hashlib.sha256(open('$vsrc', 'rb').read()).hexdigest() == '$vsha', '$vsrc: invalid checksum'"
            tar zxf $vsrc -C $vtmp
            python $vtmp/virtualenv-$vvers/virtualenv.py "$GALAXY_VIRTUAL_ENV"
            rm -rf $vtmp
        fi
    fi
fi

if [ $SET_VENV -eq 1 ]; then
    # If there is a .venv/ directory, assume it contains a virtualenv that we
    # should run this instance in.
    if [ -d "$GALAXY_VIRTUAL_ENV" ];
    then
        printf "Activating virtualenv at $GALAXY_VIRTUAL_ENV\n"
        . "$GALAXY_VIRTUAL_ENV/bin/activate"
        # Because it's a virtualenv, we assume $PYTHONPATH is unnecessary for
        # anything in the venv to work correctly, and having it set can cause
        # problems when there are conflicts with Galaxy's dependencies outside
        # the venv (e.g. virtualenv-burrito's pip and six).
        #
        # If you are skipping the venv setup we shall assume you know what
        # you're doing and will deal with any conflicts.
        unset PYTHONPATH
    fi

    if [ -z "$VIRTUAL_ENV" ]; then
        echo "ERROR: A virtualenv cannot be found. Please create a virtualenv in $GALAXY_VIRTUAL_ENV, or activate one."
        exit 1
    fi
fi

: ${GALAXY_WHEELS_INDEX_URL:="https://wheels.galaxyproject.org/simple"}
if [ $REPLACE_PIP -eq 1 ]; then
    pip_version=`pip --version | awk '{print $2}'`
    method=`python - << EOF
from pkg_resources import parse_version
from sys import stdout
if parse_version('$pip_version') >= parse_version('6.0'):
    stdout.write('req')
elif parse_version('$pip_version') >= parse_version('1.5'):
    stdout.write('wheel')
else:
    stdout.write('sdist')
EOF`
    case $method in
        req)
            pip install --no-index --find-links ${GALAXY_WHEELS_INDEX_URL}/pip --upgrade "pip==${GXPIP_VERSION}"
            ;;
        wheel)
            pip install --upgrade "https://wheels.galaxyproject.org/packages/pip-${GXPIP_VERSION}-py2.py3-none-any.whl"
            ;;
        sdist)
            pip install --upgrade "https://wheels.galaxyproject.org/packages/pip-${GXPIP_VERSION}.tar.gz"
            ;;
    esac

    # binary-compatibility.cfg may need to be created (e.g. on CentOS)
    [ -n "$VIRTUAL_ENV" -a ! -f ${VIRTUAL_ENV}/binary-compatibility.cfg ] && python ./scripts/binary_compatibility.py -o ${VIRTUAL_ENV}/binary-compatibility.cfg
fi

if [ $FETCH_WHEELS -eq 1 ]; then
    pip install -r requirements.txt --index-url ${GALAXY_WHEELS_INDEX_URL}
    GALAXY_CONDITIONAL_DEPENDENCIES=`PYTHONPATH=lib python -c "import galaxy.dependencies; print '\n'.join(galaxy.dependencies.optional('$GALAXY_CONFIG_FILE'))"`
    [ -z "$GALAXY_CONDITIONAL_DEPENDENCIES" ] || echo "$GALAXY_CONDITIONAL_DEPENDENCIES" | pip install -r /dev/stdin --index-url ${GALAXY_WHEELS_INDEX_URL}
fi

if [ $FETCH_WHEELS -eq 1 -a $DEV_WHEELS -eq 1 ]; then
    dev_requirements='./lib/galaxy/dependencies/dev-requirements.txt'
    [ -f $dev_requirements ] && pip install -r $dev_requirements --index-url ${GALAXY_WHEELS_INDEX_URL}
fi