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

[Sarah Hunt]

Hi Michael,

Thanks for the suggestion. We will ensure --AUTO triggers a fully 
automatic installation in our next release.

Best wishes,

Sarah

On 20/02/2018 23:23, Michael Yourshaw wrote:
>
> 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 <mailto:myourshaw at ucla.edu>
>
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