team_tools/bash_profile at main · Ensembl/team_tools · GitHub

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#!/bin/bash
# THIS IS NOT DESIGNED TO BE RUN - it should be sourced to set up an existing or new shell.
# -*- Shell-script -*-

# anacode environment
anacode_dir=/software/anacode

if [ -d "$anacode_dir" ]
    then

    # distro-specific directories, appended first so that their contents
    # will override the contents of distro-independent directories

    # we must use the full path to anacode_distro_code as $anacode_dir/bin
    # is not yet on $PATH

    anacode_distro_code="$( $anacode_dir/bin/anacode_distro_code )"
    if [ -n "$anacode_distro_code" ]
        then
        anacode_distro_dir="$anacode_dir/distro/$anacode_distro_code"
        if [ -d "$anacode_distro_dir" ]
            then

            PATH="\
$PATH\
:$anacode_distro_dir/bin\
"

            PERL5LIB="\
$PERL5LIB\
:$anacode_distro_dir/lib\
:$anacode_distro_dir/lib/site_perl\
"

        fi
    fi

    # choose the Perl
    if ! ( echo "$PATH" | sed -e 's/:/\n/g' | grep -q -E ^/software/perl ); then
        case "$anacode_distro_code" in
            lenny|lucid|squeeze) PATH="/software/perl-5.12.2/bin:$PATH" ;;
            precise) PATH="/software/perl-5.14.4/bin:$PATH" ;;
            trusty)  PATH="/software/perl-5.18.2/bin:$PATH" ;;
            etch) # not expecting to need this; 5.12.2 needs GLIBC_2.4
            PATH="/software/perl-5.10.1/bin:$PATH"
            ;;
            *) echo $0: Not sure which Perl we want for distro=$anacode_distro_code, take default $( which perl ) >&2 ;;
        esac
    fi

    # distro-independent directories

    echo $PATH | sed -e 's/:/\n/g' | grep -qE "^$anacode_dir/bin"'/?$' || \
        PATH="\
$PATH\
:$anacode_dir/bin\
"
    # May be set in /software/anacode/etc/profile.anacode , see ./swac-etc/

    PERL5LIB="\
$PERL5LIB\
:$anacode_dir/lib\
:$anacode_dir/lib/site_perl\
"

    export no_proxy=localhost
    export http_proxy=http://webcache.sanger.ac.uk:3128


fi # if [ -d "$anacode_dir" ]

# team_tools environment

if true &&
    [ -n "$ANACODE_TEAM_TOOLS" ] &&
    [ -d "$ANACODE_TEAM_TOOLS" ]
    then

    PATH="\
$PATH\
:$ANACODE_TEAM_TOOLS/bin\
:$ANACODE_TEAM_TOOLS/otterlace/bin\
:$ANACODE_TEAM_TOOLS/otterlace/release/scripts\
"

    PERL5LIB="\
$PERL5LIB\
:$ANACODE_TEAM_TOOLS/perl/lib\
"

fi

PERL5LIB="${PERL5LIB#:}" # in case $PERL5LIB was originally empty

export PATH PERL5LIB

CVS_RSH=ssh
export CVS_RSH

ANACODE_PERLCRITICRC="$ANACODE_TEAM_TOOLS/perl/perlcriticrc"
export ANACODE_PERLCRITICRC

umask 022

unset \
    anacode_dir \
    anacode_distro_code \