<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
</head>
<body bgcolor="#FFFFFF" text="#000000">
<p><br>
</p>
<p>Hi Michael,</p>
<p>Thanks for the suggestion. We will ensure --AUTO triggers a fully
automatic installation in our next release.<br>
</p>
Best wishes,<br>
<br>
Sarah<br>
<div class="moz-cite-prefix"><br>
On 20/02/2018 23:23, Michael Yourshaw wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CANcs_JKio+mt7FJdWtwLxSGd46xE0Uyfy8UmN3FKJASNgpVdbQ@mail.gmail.com">
<div dir="ltr">
<p
style="margin-top:0px;margin-bottom:0px;color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px">The
VEP option --AUTO should be capable of running a fully
automatic installation.</p>
<p
style="margin-top:0px;margin-bottom:0px;color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px"><br>
</p>
<p
style="margin-top:0px;margin-bottom:0px;color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px">However,
if --DESTDIR is specified, the script will pause for input,
and may exit prematurely.</p>
<p
style="margin-top:0px;margin-bottom:0px;color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px"><br>
</p>
<p
style="margin-top:0px;margin-bottom:0px;color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px">Automatic
installation may be desirable for some users who also wish to
specify a non-standard DESTDIR, <span
style="font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple
Color Emoji","Segoe UI
Emoji",NotoColorEmoji,"Segoe UI
Symbol","Android Emoji",EmojiSymbols"> for
example, if building a Singularity image</span>.</p>
<p
style="margin-top:0px;margin-bottom:0px;color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px"><br>
</p>
<p
style="margin-top:0px;margin-bottom:0px;color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px">I
suggest adding a test for $AUTO to skip the exit associated
with the PERL5LIB/PATH warning, for example:</p>
<p
style="margin-top:0px;margin-bottom:0px;color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px"><br>
</p>
<div
style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px"> <span
style="font-family:"Courier
New",monospace,serif,EmojiFont;font-size:10pt"> # check
if $DEST_DIR is default</span></div>
<div
style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px"><span
style="font-family:"Courier
New",monospace,serif,EmojiFont;font-size:10pt">
if(defined($DEST_DIR)) {</span></div>
<div
style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px"><span
style="font-family:"Courier
New",monospace,serif,EmojiFont;font-size:10pt">
print "Using non-default API installation directory
$DEST_DIR.\n";</span></div>
<div
style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px"><span
style="font-family:"Courier
New",monospace,serif,EmojiFont;font-size:10pt">
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";</span></div>
<div
style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px"><span
style="font-family:"Courier
New",monospace,serif,EmojiFont;font-size:10pt">
print "Have you \n";</span></div>
<div
style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px"><span
style="font-family:"Courier
New",monospace,serif,EmojiFont;font-size:10pt">
print "1. added $DEST_DIR to your PERL5LIB environment
variable?\n";</span></div>
<div
style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px"><span
style="font-family:"Courier
New",monospace,serif,EmojiFont;font-size:10pt">
print "2. added $DEST_DIR/htslib to your PATH environment
variable?\n";</span></div>
<div
style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px"><span
style="font-family:"Courier
New",monospace,serif,EmojiFont;font-size:10pt"> if(
$this_os eq 'darwin' && !$NO_HTSLIB) {</span></div>
<div
style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px"><span
style="font-family:"Courier
New",monospace,serif,EmojiFont;font-size:10pt">
print "3. added $DEST_DIR/htslib to your DYLD_LIBRARY_PATH
environment variable?\n";</span></div>
<div
style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px"><span
style="font-family:"Courier
New",monospace,serif,EmojiFont;font-size:10pt"> }</span></div>
<div
style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px"><span
style="font-family:"Courier
New",monospace,serif,EmojiFont;font-size:10pt">
print "(y/n): ";</span></div>
<div
style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px"><br>
</div>
<div
style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px"><span
style="font-family:"Courier
New",monospace,serif,EmojiFont;font-size:10pt"> my
$ok = <>;</span></div>
<div
style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px"><span
style="font-family:"Courier
New",monospace,serif,EmojiFont;font-size:10pt"><br>
</span></div>
<div
style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px"><span
style="font-family:"Courier
New",monospace,serif,EmojiFont;font-size:10pt"> <b> #
do not exit if AUTO</b></span></div>
<div
style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px"><span
style="font-family:"Courier
New",monospace,serif,EmojiFont;font-size:10pt">
<div><b> if($AUTO) {</b></div>
<div><b> $ok = 'y';</b></div>
<div><b> }</b></div>
<div><br>
</div>
if($ok !~ /^y/i) {</span></div>
<div
style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px"><span
style="font-family:"Courier
New",monospace,serif,EmojiFont;font-size:10pt">
print "Exiting. Please \n";</span></div>
<div
style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px"><span
style="font-family:"Courier
New",monospace,serif,EmojiFont;font-size:10pt">
print "1. add $DEST_DIR to your PERL5LIB environment
variable\n";</span></div>
<div
style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px"><span
style="font-family:"Courier
New",monospace,serif,EmojiFont;font-size:10pt">
print "2. add $DEST_DIR/htslib to your PATH environment
variable\n";</span></div>
<div
style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px"><span
style="font-family:"Courier
New",monospace,serif,EmojiFont;font-size:10pt">
if( $this_os eq 'darwin' && !$NO_HTSLIB) {</span></div>
<div
style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px"><span
style="font-family:"Courier
New",monospace,serif,EmojiFont;font-size:10pt">
print "3. add $DEST_DIR/htslib to your DYLD_LIBRARY_PATH
environment variable\n";</span></div>
<div
style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px"><span
style="font-family:"Courier
New",monospace,serif,EmojiFont;font-size:10pt"> }</span></div>
<div
style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px"><span
style="font-family:"Courier
New",monospace,serif,EmojiFont;font-size:10pt">
exit(0);</span></div>
<div
style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px"><span
style="font-family:"Courier
New",monospace,serif,EmojiFont;font-size:10pt"> }</span></div>
<div
style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px"><span
style="font-family:"Courier
New",monospace,serif,EmojiFont;font-size:10pt"> if(
! -d $DEST_DIR ) {</span></div>
<div
style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px"><span
style="font-family:"Courier
New",monospace,serif,EmojiFont;font-size:10pt">
mkdir $DEST_DIR || die "Could not make destination directory
$DEST_DIR"</span></div>
<div
style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px"><span
style="font-family:"Courier
New",monospace,serif,EmojiFont;font-size:10pt"> }</span></div>
<div
style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px"><span
style="font-family:"Courier
New",monospace,serif,EmojiFont;font-size:10pt">
$default_dir_used = 0;</span></div>
<div
style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px"><span
style="font-family:"Courier
New",monospace,serif,EmojiFont;font-size:10pt"> }</span></div>
<div
style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px"><br>
</div>
<div
style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px"><br>
</div>
<div
style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px"><br>
</div>
<div
style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px"><br>
</div>
<div>
<div class="gmail_signature">
<div dir="ltr">
<div>ॐ<br>
Michael Yourshaw<br>
<a href="mailto:myourshaw@ucla.edu" target="_blank"
moz-do-not-send="true">myourshaw@gmail.com</a><br>
<br>
This message is intended only for the use of the
addressee and may contain information that is PRIVILEGED
and CONFIDENTIAL, and/or may contain ATTORNEY WORK
PRODUCT. If you are not the intended recipient, you are
hereby notified that any dissemination of this
communication is strictly prohibited. If you have
received this communication in error, please erase all
copies of the message and its attachments and notify us
immediately. Thank you.</div>
</div>
</div>
</div>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
<pre wrap="">_______________________________________________
Dev mailing list <a class="moz-txt-link-abbreviated" href="mailto:Dev@ensembl.org">Dev@ensembl.org</a>
Posting guidelines and subscribe/unsubscribe info: <a class="moz-txt-link-freetext" href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a>
Ensembl Blog: <a class="moz-txt-link-freetext" href="http://www.ensembl.info/">http://www.ensembl.info/</a>
</pre>
</blockquote>
<br>
</body>
</html>