[ensembl-dev] VEP installer not fully automatic with --DESTDIR

[Michael Yourshaw]

The VEP option --AUTO should be capable of running a fully automatic
installation.


However, if --DESTDIR is specified, the script will pause for input, and
may exit prematurely.


Automatic installation may be desirable for some users who also wish to
specify a non-standard DESTDIR,  for example, if building a Singularity
image.


I suggest adding a test for $AUTO to skip the exit associated with the
PERL5LIB/PATH warning, for example:


  # check if $DEST_DIR is default
  if(defined($DEST_DIR)) {
    print "Using non-default API installation directory $DEST_DIR.\n";
    print "Please note this just specifies the location for downloaded API
files. The vep script will remain in its current location where ensembl-vep
was unzipped.\n";
    print "Have you \n";
    print "1. added $DEST_DIR to your PERL5LIB environment variable?\n";
    print "2. added $DEST_DIR/htslib to your PATH environment variable?\n";
    if( $this_os eq 'darwin' && !$NO_HTSLIB) {
      print "3. added $DEST_DIR/htslib to your DYLD_LIBRARY_PATH
environment variable?\n";
    }
    print "(y/n): ";

    my $ok = <>;

 *   # do not exit if AUTO*
*    if($AUTO) {*
*      $ok = 'y';*
*    }*

    if($ok !~ /^y/i) {
      print "Exiting. Please \n";
      print "1. add $DEST_DIR to your PERL5LIB environment variable\n";
      print "2. add $DEST_DIR/htslib to your PATH environment variable\n";
      if( $this_os eq 'darwin' && !$NO_HTSLIB) {
        print "3. add $DEST_DIR/htslib to your DYLD_LIBRARY_PATH
environment variable\n";
      }
      exit(0);
    }
    if( ! -d $DEST_DIR ) {
      mkdir $DEST_DIR || die "Could not make destination directory
$DEST_DIR"
    }
    $default_dir_used = 0;
  }




ॐ
Michael Yourshaw
myourshaw at gmail.com <myourshaw at ucla.edu>

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