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Re: [Gmod-ajax] Multiple Jbrowse on same server issue
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From: Justin E. <jus...@or...> - 2021-10-18 17:37:08
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I seem to have figured it out, although I don't actually understand
why...<br>
<br>
I stepped away for a couple minutes and remembered there is one
other bit for the apache config for both. Both instances have a
jbrowse/.htaccess file to control access as we don't want this data
public yet.<br>
<br>
The .htaccess for both is:<br>
Order Deny,Allow<br>
Deny from all<br>
Allow from 128.193<br>
Allow from 10<br>
Allow from 206.214.233.4<br>
<br>
128.193 is the public IP block for OSU, 10 is the private IP range
for clients at OSU. 206.214.233.4 is my public IP (Starlink, behind
CGNAT) since I work remotely.<br>
<br>
I removed the .htaccess for panoryza and now see the
"Congratulations, JBrowse on the web!", like I expect. So clearly
that is the issue.<br>
<br>
I tried putting it back and adding the 192.168 private IP range for
the server, and it still works.<br>
<br>
I'm just guessing, but think some combination of the restrictions
and the SSL config was causing it. Like the permanent redirect from
the *.80 to *.443 without having the 192.168 range in the allowed
list was somehow causing it.<br>
<br>
Anyway, thank you so much for the help, and sorry to have wasted
your time with something that appears to be a misconfiguration on my
end.<br>
<br>
Justin<br>
<br>
<div class="moz-cite-prefix">On 10/18/21 9:27 AM, Colin wrote:<br>
</div>
<blockquote type="cite" cite="mid:CA+ZENaKyjY6Mj+BbrYU=2am...@ma...">
<p><span style="color:#D73F09;">[This email originated from
outside of OSU. Use caution with links and attachments.]</span></p>
<div>
<div dir="ltr">>Of course, I could still be missing
something, but I don't see how this is an Apache issue. It
seems more like jbrowse instances are using some shared space
for something. Does it use /tmp for anything or any other
system-wide resources?
<div><br>
</div>
<div>It is important to note that JBrowse does not run any
server side scripts like php or cgi-bin perl, and so you can
generally think of the problem in terms of just accessing
plain static files in a given directory. When you visit
jbrowse in your web browser, you are just accessing static
resources e.g. plain html, js, and css files. No code is run
aside from apache just returning those files verbatim to the
client. The scripts such as setup.sh,
<a href="https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fprepare-refseqs.pl%2F&data=04%7C01%7Cjustin.elser%40oregonstate.edu%7C877964f486454881612a08d992542f71%7Cce6d05e13c5e4d6287a84c4a2713c113%7C0%7C0%7C637701712545938690%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=eEl84C7F%2BY4ZDM6Q2nMP1Pi5bUcgThcLY5g%2FEI9GXZc%3D&reserved=0" originalsrc="http://prepare-refseqs.pl/" shash="LmS6QNc32SGmeVOS3cdy1YU1BHulCKB0wzAK1s9omolknAzCzZGNSO0qPKcfQqUmIex6KVWtejnWotzZxguWGOu6LLAaAjfw3Ns0P8ZdEmfRswHMpV6KgRtONhh+hdjI9r2TdcLL2R6TgCDeTfifuYrxJF1U3HnRjaxEYyKiDBQ=" moz-do-not-send="true">prepare-refseqs.pl</a>, and <a href="https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fflatfile-to-json.pl%2F&data=04%7C01%7Cjustin.elser%40oregonstate.edu%7C877964f486454881612a08d992542f71%7Cce6d05e13c5e4d6287a84c4a2713c113%7C0%7C0%7C637701712545948650%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=MIakcIqlqM5tGWAmAhuX0zXGK1FRDYB5dV2dMj%2BakSQ%3D&reserved=0" originalsrc="http://flatfile-to-json.pl/" shash="sKF/RvMpBRGB/tR75le4dFjBYT6fCjW63nhhzyQSe3hAObcfGcYxf+jJmfY2gVD9V4KRHoMHVCL127aVUjIwWS1sy6t1u9EPHfVuSqvcglkd+HdkvrGPUWIeShodW0AztVTd4Zgu2d9wWhZT3ulcyt45h383EzXn1p3I64Tgjg8=" moz-do-not-send="true">
flatfile-to-json.pl</a> only exist to initialize your
files and add to your trackList.json (and sometimes convert
e.g. gff to json with flatfile-to-json).</div>
<div><br>
</div>
<div>If you believe your apache config is correct (we don't
have the ability to debug apache issues necessarily but it
does look like your config is correct), then one other thing
you could check for are accidental symlinks to see if for
some reason data is perhaps symlinked accidentally between
your two instances</div>
<div><br>
</div>
<div><br>
</div>
<div>-Colin</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Mon, Oct 18, 2021 at
12:08 PM Justin Elser <<a href="mailto:jus...@or..." moz-do-not-send="true">jus...@or...</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px
0.8ex;border-left:1px solid
rgb(204,204,204);padding-left:1ex">
<div>That seems like a possible cause, but I don't see
anything wrong with the Apache config. For reference, here
are all the relevant apache conf files:<br>
panoryza.conf:<br>
<VirtualHost *:80><br>
ServerAdmin <a href="mailto:el...@sc..." target="_blank" moz-do-not-send="true">
el...@sc...</a><br>
DocumentRoot /data/www/panoryza<br>
ServerName <a href="https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fpanoryza.cgrb.oregonstate.edu%2F&data=04%7C01%7Cjustin.elser%40oregonstate.edu%7C877964f486454881612a08d992542f71%7Cce6d05e13c5e4d6287a84c4a2713c113%7C0%7C0%7C637701712545958617%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=FqUyTt06T9nmlILdAJBsx3HdBOg5oXYWPCE%2F9V4TDiU%3D&reserved=0" originalsrc="http://panoryza.cgrb.oregonstate.edu/" shash="I58ngsSCTCLxgJUcZVcH+p/MHn2QjYLOxa/hS4hL0h0/Lvag+ja60HwsWp7bGVtWcv41IS524Qbds4VfpnQslgvxberbp0OftADa3aiBUTQsW77saN8sa1/TvUxnZ0/9ek9UDqc+2C1vH4h1EDG5zyW7LW2g8cAVqpiRDHzbRNo=" target="_blank" moz-do-not-send="true">
panoryza.cgrb.oregonstate.edu</a><br>
Redirect permanent / <a href="https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpanoryza.cgrb.oregonstate.edu%2F&data=04%7C01%7Cjustin.elser%40oregonstate.edu%7C877964f486454881612a08d992542f71%7Cce6d05e13c5e4d6287a84c4a2713c113%7C0%7C0%7C637701712545958617%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=NODDicDHsk%2FBZS9hUglK5iJkM%2FcjarHIvV2IGXUnF2Q%3D&reserved=0" originalsrc="https://panoryza.cgrb.oregonstate.edu/" shash="Qd6uQNNv/EKg+Oas55wBC9sqCGuqb0BNOsNZoB7OypQVjE4H5DQlgDCjLtxuCdW5YrueUpzAh4sNsndhGWjSwLjO361d8G9riJklor6ldtzj0A5dsxAuNkYWTCR/Jzyn5DLMKJozgv6B6X65ab7abJYoDfeyRhJuJCAPPxhM7EA=" target="_blank" moz-do-not-send="true">
https://panoryza.cgrb.oregonstate.edu/</a><br>
</VirtualHost><br>
<br>
panoryza-ssl.conf:<br>
<VirtualHost *:443><br>
ServerAdmin <a href="mailto:el...@sc..." target="_blank" moz-do-not-send="true">
el...@sc...</a><br>
DocumentRoot /data/www/panoryza<br>
ServerName <a href="https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fpanoryza.cgrb.oregonstate.edu%2F&data=04%7C01%7Cjustin.elser%40oregonstate.edu%7C877964f486454881612a08d992542f71%7Cce6d05e13c5e4d6287a84c4a2713c113%7C0%7C0%7C637701712545968566%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=1RDqb%2B5gcmQNiq4dmUQPyW%2Fx3y0kUp%2BfHHNhPOMDff0%3D&reserved=0" originalsrc="http://panoryza.cgrb.oregonstate.edu/" shash="lb/m4vEs02ZhkQ7x6mSRSGBMA1o05Drs+BBKPX7Bn62PDT8blVkjpg8lvqqFAAcCWJX/dNCvTTfgHNL+mMvtL8J3KQeeNz+G2XLEX3msxLWpBKoOIjazFUPw4YhUgk0Z3dF1cUYi8gIuqDzS8r/0C0+jUPLjcOSfMnoOzNYHj7I=" target="_blank" moz-do-not-send="true">
panoryza.cgrb.oregonstate.edu</a><br>
<Directory "/data/www/panoryza"><br>
Options Indexes FollowSymLinks<br>
AllowOverride All<br>
Require all granted<br>
</Directory><br>
<br>
SSLEngine on<br>
SSLProtocol All -SSLv2 -SSLv3 -TLSv1 -TLSv1.1<br>
SSLCipherSuite
ALL:!ADH:!EXPORT56:RC4+RSA:+HIGH:+MEDIUM:+LOW:+SSLv2:+EXP<br>
SSLCertificateFile
/etc/pki/tls/certs/__cgrb_oregonstate_edu_cert.cer<br>
SSLCertificateChainFile
/etc/pki/tls/certs/__cgrb_oregonstate_edu_interm.cer<br>
SSLCertificateKeyFile
/etc/pki/tls/private/cgrb.key<br>
</VirtualHost><br>
<br>
salvia.conf:<br>
<VirtualHost *:80><br>
ServerAdmin <a href="mailto:el...@sc..." target="_blank" moz-do-not-send="true">
el...@sc...</a><br>
DocumentRoot /data/www/salvia<br>
ServerName <a href="https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fsalvia.cgrb.oregonstate.edu%2F&data=04%7C01%7Cjustin.elser%40oregonstate.edu%7C877964f486454881612a08d992542f71%7Cce6d05e13c5e4d6287a84c4a2713c113%7C0%7C0%7C637701712545978527%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=3WEYeDXLKBO0By44d06v6jEZ9gMnBYDNdR0%2Fq39OsXA%3D&reserved=0" originalsrc="http://salvia.cgrb.oregonstate.edu/" shash="yQSsAGgYY4rqIq8genaFn3dcRUREWXDrtXxovzaOZiJ2zzxNc1vaYuwLEcJjOpiD88nwPualXUFH/8QcgDCHHj+UU9UHbDLHkip/UHgeNodKWwJ0V3TxDDd+jyU0Ui5yIu/y14hXpTF9lEaI58/VI1CvEILPQufqbCSL9G5nXYw=" target="_blank" moz-do-not-send="true">salvia.cgrb.oregonstate.edu</a><br>
Redirect permanent / <a href="https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsalvia.cgrb.oregonstate.edu%2F&data=04%7C01%7Cjustin.elser%40oregonstate.edu%7C877964f486454881612a08d992542f71%7Cce6d05e13c5e4d6287a84c4a2713c113%7C0%7C0%7C637701712545988471%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=RiFJ3BMchVNugZKJLo2uvss41IzBfiHqgB8J4QBa5OI%3D&reserved=0" originalsrc="https://salvia.cgrb.oregonstate.edu/" shash="fRC+eWsz+4SDxQ+mTD5E0LVqy36pkszw6ncYdha13drRgUw9aCjoCpEm+9yLCq10Xb+MLaQNxiP01tUk9GZp+AP+BSoyExAQDgkJyTKYXJ5Oy2f/F3KDXYGJLnHgavODTEpcPHtHr9h7FXV4LKXaV8AdtquuHVy8Y9cG51fTvl8=" target="_blank" moz-do-not-send="true">
https://salvia.cgrb.oregonstate.edu/</a><br>
</VirtualHost><br>
<br>
salvia-ssl.conf:<br>
<VirtualHost *:443><br>
ServerAdmin <a href="mailto:el...@sc..." target="_blank" moz-do-not-send="true">
el...@sc...</a><br>
DocumentRoot /data/www/salvia<br>
ServerName <a href="https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fsalvia.cgrb.oregonstate.edu%2F&data=04%7C01%7Cjustin.elser%40oregonstate.edu%7C877964f486454881612a08d992542f71%7Cce6d05e13c5e4d6287a84c4a2713c113%7C0%7C0%7C637701712545988471%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=tIVYhpfH3CJAenabt1Gh%2BET4nMyd0rQPbODwSrZ1utg%3D&reserved=0" originalsrc="http://salvia.cgrb.oregonstate.edu/" shash="ii+qmF62xpDA4rt7fifSZbTJsY6mFiKx762K0RGzmdOSvD5uPruwEv7BrZnpwqS2OejmPH6YSmZEZZDDg3LBLimRV6EgxcewGGhMLxtUSFjJN3iVhjUdxLul/kvKxH3wKkbKLZDg43NEGd+WnOS8tbF1gw2xY+V1olyV3cGfx4I=" target="_blank" moz-do-not-send="true">salvia.cgrb.oregonstate.edu</a><br>
<Directory "/data/www/salvia"><br>
Options Indexes FollowSymLinks<br>
AllowOverride All<br>
Require all granted<br>
</Directory><br>
<br>
SSLEngine on<br>
SSLProtocol All -SSLv2 -SSLv3 -TLSv1 -TLSv1.1<br>
SSLCipherSuite
ALL:!ADH:!EXPORT56:RC4+RSA:+HIGH:+MEDIUM:+LOW:+SSLv2:+EXP<br>
SSLCertificateFile
/etc/pki/tls/certs/__cgrb_oregonstate_edu_cert.cer<br>
SSLCertificateChainFile
/etc/pki/tls/certs/__cgrb_oregonstate_edu_interm.cer<br>
SSLCertificateKeyFile
/etc/pki/tls/private/cgrb.key<br>
</VirtualHost><br>
<br>
I've simplified them now so they don't use Aliases for
jbrowse and reloaded Apache via "systemctl reload httpd"
to ensure the new configs are being used. Same issue
still.<br>
<br>
Just to be sure there is no cross config in the paths:<br>
[elserj@floret conf.d]$ egrep "salvia|panoryza" ./*<br>
./panoryza.conf: DocumentRoot /data/www/panoryza<br>
./panoryza.conf: ServerName <a href="https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fpanoryza.cgrb.oregonstate.edu%2F&data=04%7C01%7Cjustin.elser%40oregonstate.edu%7C877964f486454881612a08d992542f71%7Cce6d05e13c5e4d6287a84c4a2713c113%7C0%7C0%7C637701712545998442%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=Ff8naesGOP4ujnqd9W%2BzLEyMY7RFcnjeSA3R4vec5pc%3D&reserved=0" originalsrc="http://panoryza.cgrb.oregonstate.edu/" shash="mtcRU6uUS7DoQIOJyuwRR5o+2vy0Cc6BW+KEvsWkyha1NPTdx8LOjin6vFMZYmT1XSGONkazZu1VsbcpUsSl8j2tppkRI5KsMDaGy1/xt1XM+FhSzTSzT6uohmY+Qn0fPjpptZUZUSAvnA21GiOmKMkC0j1d/bEpQvZYXh8Zy10=" target="_blank" moz-do-not-send="true">
panoryza.cgrb.oregonstate.edu</a><br>
./panoryza.conf: Redirect permanent / <a href="https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpanoryza.cgrb.oregonstate.edu%2F&data=04%7C01%7Cjustin.elser%40oregonstate.edu%7C877964f486454881612a08d992542f71%7Cce6d05e13c5e4d6287a84c4a2713c113%7C0%7C0%7C637701712546008394%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=fo3pqeKnm1b8cRQV3V3wUh%2F%2FXRA%2B6MPb%2F4U0e%2BxYGEw%3D&reserved=0" originalsrc="https://panoryza.cgrb.oregonstate.edu/" shash="xxkwO5immKHS/ecaErzmrv9+8JPn9YFhSTRBhMtNCuW7tUJ2C4H0rRg83ngySpkSrnZgQdMemofghACEbjQ02jTtjZAMXTzOeMrTNJP3ZO6K0P2JEwDnYa0b2IANvnMEGJmtH7DABd0eGZyNwaiGRPE88UkRJIWTaImxHDEkPqk=" target="_blank" moz-do-not-send="true">
https://panoryza.cgrb.oregonstate.edu/</a><br>
./panoryza-ssl.conf: DocumentRoot
/data/www/panoryza<br>
./panoryza-ssl.conf: ServerName <a href="https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fpanoryza.cgrb.oregonstate.edu%2F&data=04%7C01%7Cjustin.elser%40oregonstate.edu%7C877964f486454881612a08d992542f71%7Cce6d05e13c5e4d6287a84c4a2713c113%7C0%7C0%7C637701712546008394%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=H3ub8FyiBqaAZ0X8W4Qk%2FUug7ktNcPJWzE1yvA1nj8g%3D&reserved=0" originalsrc="http://panoryza.cgrb.oregonstate.edu/" shash="HjlveQGLvEVFE4sD4hcZzUG1tCuOcCyJvTFrWhvpC9kwTasiD9ve9SG493A+mGLCAcddpvuDkj2WnvNJKSpQb4sRzEgc6M5O4orGjw7xmJW6HWl4yvH6WrR9hi7uNf+McgXNeLcAvknv6MNFLJKdUSo8SljRMZNkVprJ91vaXlo=" target="_blank" moz-do-not-send="true">
panoryza.cgrb.oregonstate.edu</a><br>
./panoryza-ssl.conf: <Directory
"/data/www/panoryza"><br>
./salvia.conf: DocumentRoot /data/www/salvia<br>
./salvia.conf: ServerName <a href="https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fsalvia.cgrb.oregonstate.edu%2F&data=04%7C01%7Cjustin.elser%40oregonstate.edu%7C877964f486454881612a08d992542f71%7Cce6d05e13c5e4d6287a84c4a2713c113%7C0%7C0%7C637701712546018347%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=O26i4V3jFOg%2BuZKy%2B9IRPT9ZxgiF5aqhrRzdPfFDlCY%3D&reserved=0" originalsrc="http://salvia.cgrb.oregonstate.edu/" shash="x6W3xEFhTuzz2TqIvJiPFxbuGvY4TEJST5xqbRbpFEmLsekEMabY7F/Tkv53E+yxzAHROSkCPTG9NE4BWZPmFybDKw+lPnDAiwc1cXyscmaA1i/TP/STo8EY7MSyWpF4VDE5O4LUz4MmJtEFSopx2Kp0265GXn8uwzyeZjm1Ces=" target="_blank" moz-do-not-send="true">
salvia.cgrb.oregonstate.edu</a><br>
./salvia.conf: Redirect permanent / <a href="https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsalvia.cgrb.oregonstate.edu%2F&data=04%7C01%7Cjustin.elser%40oregonstate.edu%7C877964f486454881612a08d992542f71%7Cce6d05e13c5e4d6287a84c4a2713c113%7C0%7C0%7C637701712546018347%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=peCVTCVyQNVu8AjR1wdMligxOh7ig7r0yJH9C0flhWk%3D&reserved=0" originalsrc="https://salvia.cgrb.oregonstate.edu/" shash="kwldor1+tqZLuoq+seKjuf/qR6e0/2W78L8BO2GzhD8k/kV0XHYt+bUFaV61InKpVi+Ld6V7BQhCLYUpOmPwrpCpx+IA0Ez2TkgaRMVdA1EY5x6gk2z2Uz8O7a3ioh6WPB0cmrIVU2Pv4h65pJNywT2EqwXJPDKLX/ID7pK/SGA=" target="_blank" moz-do-not-send="true">
https://salvia.cgrb.oregonstate.edu/</a><br>
./salvia-ssl.conf: DocumentRoot /data/www/salvia<br>
./salvia-ssl.conf: ServerName <a href="https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fsalvia.cgrb.oregonstate.edu%2F&data=04%7C01%7Cjustin.elser%40oregonstate.edu%7C877964f486454881612a08d992542f71%7Cce6d05e13c5e4d6287a84c4a2713c113%7C0%7C0%7C637701712546028306%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=9YaTodI8%2BPyTgZ8fJwzA%2FpCbzxtjKox9186nbI5%2FP8A%3D&reserved=0" originalsrc="http://salvia.cgrb.oregonstate.edu/" shash="xFzrjhoF+k0krG9tSlCFn6EIAbhMfDxMVEACZHryzTV0FyPUWc/fgzYYcnRuh77ksdAzVpZ/jEX/93v+VYHSiI7zLaOfhVDcSkDP0GouNssqQ5lc46aETrJSo9pwVN4NqIRJM/EJX0Fl2KR3CNO8VguudzQnpkQbTTa43W+4fHY=" target="_blank" moz-do-not-send="true">
salvia.cgrb.oregonstate.edu</a><br>
./salvia-ssl.conf: <Directory
"/data/www/salvia"><br>
<br>
Of course, I could still be missing something, but I don't
see how this is an Apache issue. It seems more like
jbrowse instances are using some shared space for
something. Does it use /tmp for anything or any other
system-wide resources?<br>
<br>
I did look at /tmp to see if I noticed anything, and I do
see a directory that looks like it was created for npm
installation, I'm guessing it's from the ./setup.sh step,
but don't see any config stuff in there.<br>
<br>
Please let me know if I can provide any more info to help
track this down.<br>
<br>
I appreciate all the help.<br>
<br>
Thanks,<br>
Justin<br>
<br>
<div>On 10/16/21 1:05 PM, Colin wrote:<br>
</div>
<blockquote type="cite">
<p><span style="color:rgb(215,63,9)">[This email
originated from outside of OSU. Use caution with
links and attachments.]</span></p>
<div>
<div dir="ltr">
<div>Seems like this is likely an apache config
issue, hard to tell what exactly though.</div>
<div><br>
</div>
<div>Note that even using Alias and Directory
configs may be unneeded. For example, if you have
a DocumentRoot e.g.</div>
<div><br>
</div>
<blockquote class="gmail_quote" style="margin:0px
0px 0px 0.8ex;border-left:1px solid
rgb(204,204,204);padding-left:1ex">
<VirtualHost *:80><br>
DocumentRoot /var/www/html<br>
</VirtualHost><br>
</blockquote>
<div><br>
</div>
<div> </div>
<div>Then you can unzip the jbrowse folder to
/var/www/html/jbrowse and visit <a href="http://yourserver/jbrowse/" target="_blank" moz-do-not-send="true">
http://yourserver/jbrowse/</a></div>
<div><br>
</div>
<div>-Colin</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Sat, Oct 16,
2021 at 10:16 AM Justin Elser <<a href="mailto:jus...@or..." target="_blank" moz-do-not-send="true">jus...@or...</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px
0px 0px 0.8ex;border-left:1px solid
rgb(204,204,204);padding-left:1ex">
<div>Thanks for the reply. <br>
<br>
I haven't changed either of those files from the
default. Like I said, it seems to be getting the
data before I have made *any* changes. All I
have done is:<br>
unzip JBrowse-1.16.10.zip<br>
mv JBrowse-1.16.10 jbrowse<br>
cd jbrowse<br>
./setup.sh<br>
<br>
And then check it on the browser. And it's not
like it is getting *all* the data from the other
instance, no tracks show up and it doesn't even
say a "Reference sequence" is available either.
I should maybe also point out that it looks the
same even if I don't run "./setup.sh", which
seems odd to me as well. However, if I check
before doing the "mv JBrowse-1.16.10 jbrowse", I
get a 404 error, so it seems to serving the
correct directory.<br>
<br>
I also just moved things around, so now the
directories are /data/www/salvia/jbrowse and
/data/www/panoryza/jbrowse, just because it was
confusing having the salvia one in
/data/www/jbrowse/jbrowse, and I see the same
issue after reinstalling it in panoryza again.<br>
<br>
I'm attaching the conf files anyway, in case it
helps, but they should be identical to the ones
in the zip file.<br>
<br>
Like I said, I'm confused why it is doing this,
I don't see any way the 2 instances are
connected, other than the fact they are on the
same server.<br>
<br>
Side note, nice to see you're still working with
GMOD Scott!<br>
<br>
Please let me know what more info I can provide.<br>
<br>
Justin<br>
<br>
<div>On 10/15/21 3:05 PM, Scott Cain wrote:<br>
</div>
<blockquote type="cite">
<p><span style="color:rgb(215,63,9)">[This
email originated from outside of OSU. Use
caution with links and attachments.]</span></p>
<div>
<div dir="ltr">Hi Justin,<br>
<br>
<div>I imagine it's a jbrowse
configuration issue, like the config for
the panoryza jbrowse is looking in
/data/www/jbrowse/jbrowse for a data
directory. I bet there is some place
where you think it's using a relative
url when it's really using a file path.
Can you post both of your jbrowse.conf
and/or jbrowse_conf.json files?</div>
<div><br>
</div>
<div>Scott</div>
<div><br>
</div>
<br>
<br>
On Fri, Oct 15, 2021 at 3:00 PM Justin
Elser <<a href="mailto:jus...@or..." target="_blank" moz-do-not-send="true">jus...@or...</a>>
wrote:<br>
><br>
> Hello,<br>
><br>
> Hope this is the appropriate place to
ask this, but I'm having an issue with
having multiple Jbrowse (1.16.10)
instances running on the same apache
server. They are in separate vhosts though
and being served from different domains.<br>
><br>
> I have had one setup for almost a
year now and it works fine. However, I am
now trying to set up another one for a
different species, and I thought it would
be easiest to just do a fresh install in a
new directory. However, after unzipping
and running ./setup.sh, instead of seeing
this screen:<br>
><br>
><br>
> I see this:<br>
><br>
><br>
> Like it is already loaded with some
data, even though I haven't added any yet.
Also, the location in the dropdown "Sh6"
appears to be from the data loaded for the
other species (Salvia hispanica - chia).<br>
><br>
> I've tried to go ahead and load my
reference data (this new one is for rice),
and I get the "Reference sequence" track
but it always has "No sequence available"
and the "loc=" still references the "Sh6"
instead of "Chr1".<br>
><br>
> I've also found that if I follow the
exact same steps, but on a different
machine that doesn't already have a
jbrowse instance installed, it works
exactly as I expect, so I'm pretty sure it
is trying to read the wrong data for some
reason.<br>
><br>
> For now, both sites are restricted to
only be visible from some IP addresses,
but I can open it up temporarily if it
would help.<br>
><br>
> Also, just in case it helps, here are
the relevant bits of the Apache vhost
entries for both:<br>
> The one that works:<br>
> /etc/httpd/conf.d/salvia.conf<br>
><br>
> Alias /jbrowse
"/data/www/jbrowse/jbrowse"<br>
><br>
> <Directory
"/data/www/jbrowse/jbrowse"><br>
><br>
> AllowOverride All<br>
><br>
> Require all granted<br>
><br>
> </Directory><br>
><br>
><br>
> The one that doesn't work:<br>
> /etc/httpd/conf.d/panoryza-ssl.conf<br>
><br>
> Alias /jbrowse
"/data/www/panoryza/jbrowse"<br>
><br>
> <Directory
"/data/www/panoryza/jbrowse"><br>
><br>
> AllowOverride All<br>
><br>
> Require all granted<br>
><br>
> </Directory><br>
><br>
><br>
><br>
> I would appreciate any help in
figuring out what I am doing wrong or how
to fix this.<br>
><br>
> Thanks,<br>
> Justin Elser<br>
><br>
> -- <br>
>
**********************************************************<br>
> *
*<br>
> * Justin Elser
*<br>
> * Computational Biology Post Doc
*<br>
> * Dept. of Botany and Plant
Pathology *<br>
> * Oregon State University
*<br>
> *
*<br>
> * email: <a href="mailto:el...@sc..." target="_blank" moz-do-not-send="true">el...@sc...</a>
*<br>
> * internet: <a href="https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.science.oregonstate.edu%2F~elserj&data=04%7C01%7Cjustin.elser%40oregonstate.edu%7C877964f486454881612a08d992542f71%7Cce6d05e13c5e4d6287a84c4a2713c113%7C0%7C0%7C637701712546038250%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=sTWliWZL4r9AZI8wxWVsx%2B%2BB1GkmzareibIkQw5zmUc%3D&reserved=0" originalsrc="http://www.science.oregonstate.edu/~elserj" shash="lC2iqCoo9/yAid7AtF8Qk48sGz/Qg6XLgOFVjbxiDkgq8PBb1B6Unoz6j64Mclf80SpUoo/qDG9xWkn0M79GlVC/lBYfMwUI++/XwuSnyFWkcOcumNSO39OBrXNoxrskqRMs+pfKII0NUkFuuiQsoMvrfYu1N2O3L3/z+4t43+4=" target="_blank" moz-do-not-send="true">
www.science.oregonstate.edu/~elserj</a>
*<br>
> *
*<br>
>
**********************************************************<br>
><br>
>
_______________________________________________<br>
> Gmod-ajax mailing list<br>
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<br>
<br>
--<br>
------------------------------------------------------------------------<br>
Scott Cain, Ph. D.
scott at scottcain dot net<br>
GMOD Coordinator (<a href="https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fgmod.org%2F&data=04%7C01%7Cjustin.elser%40oregonstate.edu%7C877964f486454881612a08d992542f71%7Cce6d05e13c5e4d6287a84c4a2713c113%7C0%7C0%7C637701712546048209%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=8JNRE29TzB7CZ8zQ4lsPjyvk48ph4gWWVel%2BNbR2f8g%3D&reserved=0" originalsrc="http://gmod.org/" shash="r4wgojyNMEBtxQLo+DvDcBhM7yaj6D2ZRrq+VQMDqmasz1jYc4LxA3rDBRgs7EWiuHjqsYahQenkKvHUZojO7cVafhTZ8skvjL8ycJ2SVi1AHmwj9dCSqt+/edjxpC0AherKVJMG3GXtqurHNcjnQc8t0pB/ARE60hz9pWy5LBY=" target="_blank" moz-do-not-send="true">http://gmod.org/</a>)
216-392-3087<br>
Ontario Institute for Cancer Research</div>
</div>
</blockquote>
<br>
<pre cols="72">--
**********************************************************
* *
* Justin Elser *
* Computational Biology Post Doc *
* Dept. of Botany and Plant Pathology *
* Oregon State University *
* *
* email: <a href="mailto:el...@sc..." target="_blank" moz-do-not-send="true">el...@sc...</a> *
* internet: <a href="https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.science.oregonstate.edu%2F~elserj&data=04%7C01%7Cjustin.elser%40oregonstate.edu%7C877964f486454881612a08d992542f71%7Cce6d05e13c5e4d6287a84c4a2713c113%7C0%7C0%7C637701712546048209%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=Dbjukh44DaLYFIX0VgUN7neVuP%2BZcnxqoUvuN%2BvltLM%3D&reserved=0" originalsrc="http://www.science.oregonstate.edu/~elserj" shash="EDXcFqCDp1rUUZCWwI5Qyd6C2kXgGKWOpx1QuTjMJmYgHuuQaUCzoyW6sZRHodGPfblYL8FyyZqFSYpk6fEEKxCQgIewCOmfb+YW5Ovy16yuhRJTAjaHSAGtxzPyopBSVHJBpfzMgb8MZuAqV2MObqwBNC2YyXY2ElqYvmmt4Xs=" target="_blank" moz-do-not-send="true">www.science.oregonstate.edu/~elserj</a> *
* *
**********************************************************
</pre>
</div>
_______________________________________________<br>
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</blockquote>
</div>
</div>
</blockquote>
<br>
<pre cols="72">--
**********************************************************
* *
* Justin Elser *
* Computational Biology Post Doc *
* Dept. of Botany and Plant Pathology *
* Oregon State University *
* *
* email: <a href="mailto:el...@sc..." target="_blank" moz-do-not-send="true">el...@sc...</a> *
* internet: <a href="https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.science.oregonstate.edu%2F~elserj&data=04%7C01%7Cjustin.elser%40oregonstate.edu%7C877964f486454881612a08d992542f71%7Cce6d05e13c5e4d6287a84c4a2713c113%7C0%7C0%7C637701712546068125%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=VEKrAYBeP0SqPodkesrjcfbt7WNzmUVMpevApCdHwaw%3D&reserved=0" originalsrc="http://www.science.oregonstate.edu/~elserj" shash="wfoFPU9B4pUcpfUOP0oqbuEXkXpcxCmU2DJTBaivoRGZf974fWRdAQTFsz1yRMHZZ5YDZswPkxsd74PQVuk0iUAAFpPLgh4gXiadaFa/NCaqSaKosHXLVDZoTfcijBwIbpNZ7332YUUDIfcC8prD7TRYWAnv0KkjgkiMkCwPsps=" target="_blank" moz-do-not-send="true">www.science.oregonstate.edu/~elserj</a> *
* *
**********************************************************
</pre>
</div>
</blockquote>
</div>
</div>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
**********************************************************
* *
* Justin Elser *
* Computational Biology Post Doc *
* Dept. of Botany and Plant Pathology *
* Oregon State University *
* *
* email: <a class="moz-txt-link-abbreviated" href="mailto:el...@sc...">el...@sc...</a> *
* internet: <a class="moz-txt-link-abbreviated" href="http://www.science.oregonstate.edu/~elserj">www.science.oregonstate.edu/~elserj</a> *
* *
**********************************************************
</pre>
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