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From: Garrett S. <ste...@gm...> - 2021-10-27 17:58:01
|
Hi Uday, Are the reference sequence names in the FASTA the same ones as used in the GFF3? (i.e., it looks like your FASTA uses "chr_001", does that match what's in the GFF3 file?) A mismatch there is often a cause of an empty display. If they are not the same, you can add aliasing as described here: https://jbrowse.org/jb2/docs/config_guide/#configuring-reference-name-aliasing . Best, Garrett On Wed, Oct 27, 2021 at 9:07 AM Uday Sai Reddy Ambati via Gmod-ajax < gmo...@li...> wrote: > Hello, > > Hope you are doing well. I have a question regarding JBrowse. I tried > JBrowse using this guide(JBrowse 2 guide > <https://jbrowse.org/jb2/jbrowse2.pdf>). I am able to run JBrowse on my > computer. I uploaded a gff3 file and a fasta file. But I couldn't see > anything in the display part. So Can you help me see them? I am attaching a > screenshot of it. So please let me know what to do next in order to display > them. > > Thank you, > Uday Ambati. > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > |
|
From: Scott C. <sc...@sc...> - 2021-10-27 17:04:02
|
Hi Uday, My first guess is that there is an inconsistency between the name of the sequences in the fasta file and the identifier used in the GFF. Can you send a sample of each (we don't need the sequence from the fasta, just the ">" lines). For example, it looks like your chromosome is named "chr_001" in your fasta file. If it's referred to as "chr1" or "chr01" or "1" in your GFF, JBrowse won't be able to tell they are the same. There is a way to work around that, though, with an alias file. If you need help with that let us know. Also, in general, if you're having problems with JBrowse, it's a good idea to look in the javascript console for your browser. Is there anything there that might help point to the problem? Scott On Wed, Oct 27, 2021 at 8:07 AM Uday Sai Reddy Ambati via Gmod-ajax < gmo...@li...> wrote: > Hello, > > Hope you are doing well. I have a question regarding JBrowse. I tried > JBrowse using this guide(JBrowse 2 guide > <https://jbrowse.org/jb2/jbrowse2.pdf>). I am able to run JBrowse on my > computer. I uploaded a gff3 file and a fasta file. But I couldn't see > anything in the display part. So Can you help me see them? I am attaching a > screenshot of it. So please let me know what to do next in order to display > them. > > Thank you, > Uday Ambati. > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research |
|
From: Uday S. R. A. <ua...@ma...> - 2021-10-27 04:32:04
|
Hello, Hope you are doing well. I have a question regarding JBrowse. I tried JBrowse using this guide(JBrowse 2 guide <https://jbrowse.org/jb2/jbrowse2.pdf>). I am able to run JBrowse on my computer. I uploaded a gff3 file and a fasta file. But I couldn't see anything in the display part. So Can you help me see them? I am attaching a screenshot of it. So please let me know what to do next in order to display them. Thank you, Uday Ambati. |
|
From: Justin E. <jus...@or...> - 2021-10-18 17:37:08
|
<html><head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
</head>
<body>
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>
> <a href="mailto:Gmo...@li..." target="_blank" moz-do-not-send="true">Gmo...@li...</a><br>
> <a href="https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fgmod-ajax&data=04%7C01%7Cjustin.elser%40oregonstate.edu%7C877964f486454881612a08d992542f71%7Cce6d05e13c5e4d6287a84c4a2713c113%7C0%7C0%7C637701712546038250%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=Ny3ruMJfHwUW64v10lOBbtAjj%2B0mEHOMNlt8Cwl6ELs%3D&reserved=0" originalsrc="https://lists.sourceforge.net/lists/listinfo/gmod-ajax" shash="loOFudi4J2SZVGk1WSOcPQUkNtsZWiFgORuks7XoPAPD8LkkT9xkyoYcMWqDNkyD6SzV5iFo3afTqcb2cuoQCSGb9fBj1BrDu6iRHK59CBgsmC5iOkTivW3v19/jYCwJVCeYGdO9QLfaOwWEgNQuCOwN7J2bU9IksRWnheu8FkI=" target="_blank" moz-do-not-send="true">
https://lists.sourceforge.net/lists/listinfo/gmod-ajax</a><br>
<br>
<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> *
* *
**********************************************************
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<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>
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</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> *
* *
**********************************************************
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|
|
From: Colin <col...@gm...> - 2021-10-18 16:27:39
|
>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? 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, prepare-refseqs.pl, and flatfile-to-json.pl only exist to initialize your files and add to your trackList.json (and sometimes convert e.g. gff to json with flatfile-to-json). 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 -Colin On Mon, Oct 18, 2021 at 12:08 PM Justin Elser <jus...@or...> wrote: > 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: > panoryza.conf: > <VirtualHost *:80> > ServerAdmin el...@sc... > DocumentRoot /data/www/panoryza > ServerName panoryza.cgrb.oregonstate.edu > Redirect permanent / https://panoryza.cgrb.oregonstate.edu/ > </VirtualHost> > > panoryza-ssl.conf: > <VirtualHost *:443> > ServerAdmin el...@sc... > DocumentRoot /data/www/panoryza > ServerName panoryza.cgrb.oregonstate.edu > <Directory "/data/www/panoryza"> > Options Indexes FollowSymLinks > AllowOverride All > Require all granted > </Directory> > > SSLEngine on > SSLProtocol All -SSLv2 -SSLv3 -TLSv1 -TLSv1.1 > SSLCipherSuite > ALL:!ADH:!EXPORT56:RC4+RSA:+HIGH:+MEDIUM:+LOW:+SSLv2:+EXP > SSLCertificateFile > /etc/pki/tls/certs/__cgrb_oregonstate_edu_cert.cer > SSLCertificateChainFile > /etc/pki/tls/certs/__cgrb_oregonstate_edu_interm.cer > SSLCertificateKeyFile /etc/pki/tls/private/cgrb.key > </VirtualHost> > > salvia.conf: > <VirtualHost *:80> > ServerAdmin el...@sc... > DocumentRoot /data/www/salvia > ServerName salvia.cgrb.oregonstate.edu > Redirect permanent / https://salvia.cgrb.oregonstate.edu/ > </VirtualHost> > > salvia-ssl.conf: > <VirtualHost *:443> > ServerAdmin el...@sc... > DocumentRoot /data/www/salvia > ServerName salvia.cgrb.oregonstate.edu > <Directory "/data/www/salvia"> > Options Indexes FollowSymLinks > AllowOverride All > Require all granted > </Directory> > > SSLEngine on > SSLProtocol All -SSLv2 -SSLv3 -TLSv1 -TLSv1.1 > SSLCipherSuite > ALL:!ADH:!EXPORT56:RC4+RSA:+HIGH:+MEDIUM:+LOW:+SSLv2:+EXP > SSLCertificateFile > /etc/pki/tls/certs/__cgrb_oregonstate_edu_cert.cer > SSLCertificateChainFile > /etc/pki/tls/certs/__cgrb_oregonstate_edu_interm.cer > SSLCertificateKeyFile /etc/pki/tls/private/cgrb.key > </VirtualHost> > > 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. > > Just to be sure there is no cross config in the paths: > [elserj@floret conf.d]$ egrep "salvia|panoryza" ./* > ./panoryza.conf: DocumentRoot /data/www/panoryza > ./panoryza.conf: ServerName panoryza.cgrb.oregonstate.edu > ./panoryza.conf: Redirect permanent / > https://panoryza.cgrb.oregonstate.edu/ > ./panoryza-ssl.conf: DocumentRoot /data/www/panoryza > ./panoryza-ssl.conf: ServerName panoryza.cgrb.oregonstate.edu > ./panoryza-ssl.conf: <Directory "/data/www/panoryza"> > ./salvia.conf: DocumentRoot /data/www/salvia > ./salvia.conf: ServerName salvia.cgrb.oregonstate.edu > ./salvia.conf: Redirect permanent / https://salvia.cgrb.oregonstate.edu/ > ./salvia-ssl.conf: DocumentRoot /data/www/salvia > ./salvia-ssl.conf: ServerName salvia.cgrb.oregonstate.edu > ./salvia-ssl.conf: <Directory "/data/www/salvia"> > > 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? > > 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. > > Please let me know if I can provide any more info to help track this down. > > I appreciate all the help. > > Thanks, > Justin > > On 10/16/21 1:05 PM, Colin wrote: > > [This email originated from outside of OSU. Use caution with links and > attachments.] > Seems like this is likely an apache config issue, hard to tell what > exactly though. > > Note that even using Alias and Directory configs may be unneeded. For > example, if you have a DocumentRoot e.g. > > <VirtualHost *:80> >> DocumentRoot /var/www/html >> </VirtualHost> >> > > > Then you can unzip the jbrowse folder to /var/www/html/jbrowse and visit > http://yourserver/jbrowse/ > > -Colin > > On Sat, Oct 16, 2021 at 10:16 AM Justin Elser < > jus...@or...> wrote: > >> Thanks for the reply. >> >> 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: >> unzip JBrowse-1.16.10.zip >> mv JBrowse-1.16.10 jbrowse >> cd jbrowse >> ./setup.sh >> >> 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. >> >> 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. >> >> I'm attaching the conf files anyway, in case it helps, but they should be >> identical to the ones in the zip file. >> >> 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. >> >> Side note, nice to see you're still working with GMOD Scott! >> >> Please let me know what more info I can provide. >> >> Justin >> >> On 10/15/21 3:05 PM, Scott Cain wrote: >> >> [This email originated from outside of OSU. Use caution with links and >> attachments.] >> Hi Justin, >> >> 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? >> >> Scott >> >> >> >> On Fri, Oct 15, 2021 at 3:00 PM Justin Elser < >> jus...@or...> wrote: >> > >> > Hello, >> > >> > 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. >> > >> > 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: >> > >> > >> > I see this: >> > >> > >> > 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). >> > >> > 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". >> > >> > 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. >> > >> > 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. >> > >> > Also, just in case it helps, here are the relevant bits of the Apache >> vhost entries for both: >> > The one that works: >> > /etc/httpd/conf.d/salvia.conf >> > >> > Alias /jbrowse "/data/www/jbrowse/jbrowse" >> > >> > <Directory "/data/www/jbrowse/jbrowse"> >> > >> > AllowOverride All >> > >> > Require all granted >> > >> > </Directory> >> > >> > >> > The one that doesn't work: >> > /etc/httpd/conf.d/panoryza-ssl.conf >> > >> > Alias /jbrowse "/data/www/panoryza/jbrowse" >> > >> > <Directory "/data/www/panoryza/jbrowse"> >> > >> > AllowOverride All >> > >> > Require all granted >> > >> > </Directory> >> > >> > >> > >> > I would appreciate any help in figuring out what I am doing wrong or >> how to fix this. >> > >> > Thanks, >> > Justin Elser >> > >> > -- >> > ********************************************************** >> > * * >> > * Justin Elser * >> > * Computational Biology Post Doc * >> > * Dept. of Botany and Plant Pathology * >> > * Oregon State University * >> > * * >> > * email: el...@sc... * >> > * internet: www.science.oregonstate.edu/~elserj >> <https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.science.oregonstate.edu%2F~elserj&data=04%7C01%7Cjustin.elser%40oregonstate.edu%7C5a328a1e0d8e4cf6b77808d990e06552%7Cce6d05e13c5e4d6287a84c4a2713c113%7C0%7C0%7C637700116465366407%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=pGbYnlB79VQetdGfUjkm59%2BtubeYMc7OdN%2FdhVAAnkc%3D&reserved=0> >> * >> > * * >> > ********************************************************** >> > >> > _______________________________________________ >> > Gmod-ajax mailing list >> > Gmo...@li... >> > https://lists.sourceforge.net/lists/listinfo/gmod-ajax >> <https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fgmod-ajax&data=04%7C01%7Cjustin.elser%40oregonstate.edu%7C5a328a1e0d8e4cf6b77808d990e06552%7Cce6d05e13c5e4d6287a84c4a2713c113%7C0%7C0%7C637700116465376364%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=jKu7W8DMRVjEUzItsef4Fv5%2BVNOSsUrqrtqFdJCh0sM%3D&reserved=0> >> >> >> >> -- >> ------------------------------------------------------------------------ >> Scott Cain, Ph. D. scott at scottcain >> dot net >> GMOD Coordinator (http://gmod.org/ >> <https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fgmod.org%2F&data=04%7C01%7Cjustin.elser%40oregonstate.edu%7C5a328a1e0d8e4cf6b77808d990e06552%7Cce6d05e13c5e4d6287a84c4a2713c113%7C0%7C0%7C637700116465376364%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=9S%2FFDN7hDo67QFbgA%2FJxtd8lEcu2vpKBA7cYN4Ehb4U%3D&reserved=0>) >> 216-392-3087 >> Ontario Institute for Cancer Research >> >> >> -- >> ********************************************************** >> * * >> * Justin Elser * >> * Computational Biology Post Doc * >> * Dept. of Botany and Plant Pathology * >> * Oregon State University * >> * * >> * email: el...@sc... * >> * internet: www.science.oregonstate.edu/~elserj <https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.science.oregonstate.edu%2F~elserj&data=04%7C01%7Cjustin.elser%40oregonstate.edu%7C5a328a1e0d8e4cf6b77808d990e06552%7Cce6d05e13c5e4d6287a84c4a2713c113%7C0%7C0%7C637700116465386319%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=W3QxyG2F7HHZ0stVeaUZz%2BHQZShDZI3%2FGvSXrl%2FNE%2FM%3D&reserved=0> * >> * * >> ********************************************************** >> >> _______________________________________________ >> Gmod-ajax mailing list >> Gmo...@li... >> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >> <https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fgmod-ajax&data=04%7C01%7Cjustin.elser%40oregonstate.edu%7C5a328a1e0d8e4cf6b77808d990e06552%7Cce6d05e13c5e4d6287a84c4a2713c113%7C0%7C0%7C637700116465386319%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=4%2FnTLOM9I2lMMLOd%2BJ4oXk%2Fn3GQSU9lZQPw0tbGhxIg%3D&reserved=0> >> > > -- > ********************************************************** > * * > * Justin Elser * > * Computational Biology Post Doc * > * Dept. of Botany and Plant Pathology * > * Oregon State University * > * * > * email: el...@sc... * > * internet: www.science.oregonstate.edu/~elserj * > * * > ********************************************************** > > |
|
From: Justin E. <jus...@or...> - 2021-10-18 16:24:12
|
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<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
</head>
<body>
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 class="moz-txt-link-abbreviated" href="mailto:el...@sc...">el...@sc...</a><br>
DocumentRoot /data/www/panoryza<br>
ServerName panoryza.cgrb.oregonstate.edu<br>
Redirect permanent / <a class="moz-txt-link-freetext" href="https://panoryza.cgrb.oregonstate.edu/">https://panoryza.cgrb.oregonstate.edu/</a><br>
</VirtualHost><br>
<br>
panoryza-ssl.conf:<br>
<VirtualHost *:443><br>
ServerAdmin <a class="moz-txt-link-abbreviated" href="mailto:el...@sc...">el...@sc...</a><br>
DocumentRoot /data/www/panoryza<br>
ServerName panoryza.cgrb.oregonstate.edu<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 class="moz-txt-link-abbreviated" href="mailto:el...@sc...">el...@sc...</a><br>
DocumentRoot /data/www/salvia<br>
ServerName salvia.cgrb.oregonstate.edu<br>
Redirect permanent / <a class="moz-txt-link-freetext" href="https://salvia.cgrb.oregonstate.edu/">https://salvia.cgrb.oregonstate.edu/</a><br>
</VirtualHost><br>
<br>
salvia-ssl.conf:<br>
<VirtualHost *:443><br>
ServerAdmin <a class="moz-txt-link-abbreviated" href="mailto:el...@sc...">el...@sc...</a><br>
DocumentRoot /data/www/salvia<br>
ServerName salvia.cgrb.oregonstate.edu<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 panoryza.cgrb.oregonstate.edu<br>
./panoryza.conf: Redirect permanent /
<a class="moz-txt-link-freetext" href="https://panoryza.cgrb.oregonstate.edu/">https://panoryza.cgrb.oregonstate.edu/</a><br>
./panoryza-ssl.conf: DocumentRoot /data/www/panoryza<br>
./panoryza-ssl.conf: ServerName panoryza.cgrb.oregonstate.edu<br>
./panoryza-ssl.conf: <Directory "/data/www/panoryza"><br>
./salvia.conf: DocumentRoot /data/www/salvia<br>
./salvia.conf: ServerName salvia.cgrb.oregonstate.edu<br>
./salvia.conf: Redirect permanent /
<a class="moz-txt-link-freetext" href="https://salvia.cgrb.oregonstate.edu/">https://salvia.cgrb.oregonstate.edu/</a><br>
./salvia-ssl.conf: DocumentRoot /data/www/salvia<br>
./salvia-ssl.conf: ServerName salvia.cgrb.oregonstate.edu<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 class="moz-cite-prefix">On 10/16/21 1:05 PM, Colin wrote:<br>
</div>
<blockquote type="cite" cite="mid:CA+ZENaKuuw5rXJMgmXxF5neugrcLT4GZqN_K=W0E...@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">
<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/" 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..." 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%7C5a328a1e0d8e4cf6b77808d990e06552%7Cce6d05e13c5e4d6287a84c4a2713c113%7C0%7C0%7C637700116465366407%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=pGbYnlB79VQetdGfUjkm59%2BtubeYMc7OdN%2FdhVAAnkc%3D&reserved=0" originalsrc="http://www.science.oregonstate.edu/~elserj" shash="h8bbrUwnW412dkewLt6vvnvnqAaIBtZsyIkHgsir9siCuDT/vdp3ReQVnczNn0jgtwv7XYsaPWxuk6WgV3JyfqVq7rczwi8C6AR5FXcZMq2aUUTTPt3xwQJNrAng+V246NrHsM2Og8qobvAG07IB+qVjornz2cWTUY9mTPyShyE=" target="_blank" moz-do-not-send="true">
www.science.oregonstate.edu/~elserj</a> *<br>
> *
*<br>
>
**********************************************************<br>
><br>
> _______________________________________________<br>
> Gmod-ajax mailing list<br>
> <a href="mailto:Gmo...@li..." target="_blank" moz-do-not-send="true">Gmo...@li...</a><br>
> <a href="https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fgmod-ajax&data=04%7C01%7Cjustin.elser%40oregonstate.edu%7C5a328a1e0d8e4cf6b77808d990e06552%7Cce6d05e13c5e4d6287a84c4a2713c113%7C0%7C0%7C637700116465376364%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=jKu7W8DMRVjEUzItsef4Fv5%2BVNOSsUrqrtqFdJCh0sM%3D&reserved=0" originalsrc="https://lists.sourceforge.net/lists/listinfo/gmod-ajax" shash="egpHoEWjaweysE42YMXc/Y1aqtjtm/HSo4Gv7V2lj3g3hyssZDkpDVlLJhO1RaarNkB+NDoU3mkDzPjvKSKQiee4mN1Zu7P/M7TjV9keuj/M2G6t1aqsTwwrj2Z0/o4o0Np0z63SfKd9kakOYGKgVndYQz8ruNfmd/ccbm6PUQI=" target="_blank" moz-do-not-send="true">
https://lists.sourceforge.net/lists/listinfo/gmod-ajax</a><br>
<br>
<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%7C5a328a1e0d8e4cf6b77808d990e06552%7Cce6d05e13c5e4d6287a84c4a2713c113%7C0%7C0%7C637700116465376364%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=9S%2FFDN7hDo67QFbgA%2FJxtd8lEcu2vpKBA7cYN4Ehb4U%3D&reserved=0" originalsrc="http://gmod.org/" shash="ex56K8yg/Ni86Flbcl86Lv8waMarO/AibxLsurMRqRZ0xmmTFLlobYogJGh9o6QYkkCvCFep0Z/abUIai9Xe0il5FIQuu3JFlIQKDIWVGh3cld72E9k7g725UoFyKKlsR4h3rbPlzUYXJ9UW28XFqXlHqZEuay5ANoep/hMiRc0=" 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%7C5a328a1e0d8e4cf6b77808d990e06552%7Cce6d05e13c5e4d6287a84c4a2713c113%7C0%7C0%7C637700116465386319%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=W3QxyG2F7HHZ0stVeaUZz%2BHQZShDZI3%2FGvSXrl%2FNE%2FM%3D&reserved=0" originalsrc="http://www.science.oregonstate.edu/~elserj" shash="o+Qb76v+sTF778faCAw6YuK2/bzPy3LTsK23sO8LJyefbkfAiY6WkJaYTXV5kpceGp9xQMq9OIdeB7DbDXhCSBf30WY6h3hLr3fbXtdKx3kG2po+c3DlVXYEOuyvq3d4aWF0BuiG8a0w9sWzZd3OJzBUo1LVJBUvuaAWvRXEprc=" target="_blank" moz-do-not-send="true">www.science.oregonstate.edu/~elserj</a> *
* *
**********************************************************
</pre>
</div>
_______________________________________________<br>
Gmod-ajax mailing list<br>
<a href="mailto:Gmo...@li..." target="_blank" moz-do-not-send="true">Gmo...@li...</a><br>
<a href="https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fgmod-ajax&data=04%7C01%7Cjustin.elser%40oregonstate.edu%7C5a328a1e0d8e4cf6b77808d990e06552%7Cce6d05e13c5e4d6287a84c4a2713c113%7C0%7C0%7C637700116465386319%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=4%2FnTLOM9I2lMMLOd%2BJ4oXk%2Fn3GQSU9lZQPw0tbGhxIg%3D&reserved=0" originalsrc="https://lists.sourceforge.net/lists/listinfo/gmod-ajax" shash="C0cqiW70OUjIS7zZg8Qkcd4zz5JigBJKgNhkX3EtTcPkCXnp2VJeykuvzRuNgqOS4ulJDvYHrVsUMEtvFqddmr16DONFJNqNADqYPOOC0igKSLC8cQtgy3+vQDkPSNC1f6MKwJWuCDNatVIihpM67kadMws42BKHSJCsNKjLmRQ=" rel="noreferrer" target="_blank" moz-do-not-send="true">https://lists.sourceforge.net/lists/listinfo/gmod-ajax</a><br>
</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>
</body>
</html>
|
|
From: Colin <col...@gm...> - 2021-10-16 20:06:16
|
Seems like this is likely an apache config issue, hard to tell what exactly though. Note that even using Alias and Directory configs may be unneeded. For example, if you have a DocumentRoot e.g. <VirtualHost *:80> > DocumentRoot /var/www/html > </VirtualHost> > Then you can unzip the jbrowse folder to /var/www/html/jbrowse and visit http://yourserver/jbrowse/ -Colin On Sat, Oct 16, 2021 at 10:16 AM Justin Elser <jus...@or...> wrote: > Thanks for the reply. > > 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: > unzip JBrowse-1.16.10.zip > mv JBrowse-1.16.10 jbrowse > cd jbrowse > ./setup.sh > > 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. > > 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. > > I'm attaching the conf files anyway, in case it helps, but they should be > identical to the ones in the zip file. > > 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. > > Side note, nice to see you're still working with GMOD Scott! > > Please let me know what more info I can provide. > > Justin > > On 10/15/21 3:05 PM, Scott Cain wrote: > > [This email originated from outside of OSU. Use caution with links and > attachments.] > Hi Justin, > > 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? > > Scott > > > > On Fri, Oct 15, 2021 at 3:00 PM Justin Elser <jus...@or...> > wrote: > > > > Hello, > > > > 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. > > > > 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: > > > > > > I see this: > > > > > > 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). > > > > 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". > > > > 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. > > > > 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. > > > > Also, just in case it helps, here are the relevant bits of the Apache > vhost entries for both: > > The one that works: > > /etc/httpd/conf.d/salvia.conf > > > > Alias /jbrowse "/data/www/jbrowse/jbrowse" > > > > <Directory "/data/www/jbrowse/jbrowse"> > > > > AllowOverride All > > > > Require all granted > > > > </Directory> > > > > > > The one that doesn't work: > > /etc/httpd/conf.d/panoryza-ssl.conf > > > > Alias /jbrowse "/data/www/panoryza/jbrowse" > > > > <Directory "/data/www/panoryza/jbrowse"> > > > > AllowOverride All > > > > Require all granted > > > > </Directory> > > > > > > > > I would appreciate any help in figuring out what I am doing wrong or how > to fix this. > > > > Thanks, > > Justin Elser > > > > -- > > ********************************************************** > > * * > > * Justin Elser * > > * Computational Biology Post Doc * > > * Dept. of Botany and Plant Pathology * > > * Oregon State University * > > * * > > * email: el...@sc... * > > * internet: www.science.oregonstate.edu/~elserj > <https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.science.oregonstate.edu%2F~elserj&data=04%7C01%7Cjustin.elser%40oregonstate.edu%7C550a37b3ec78421a66ed08d99027fc9d%7Cce6d05e13c5e4d6287a84c4a2713c113%7C0%7C0%7C637699324131632320%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=QKpnruDgVGVi4knHL%2Feu8EgMcZ%2FimMJKFrWsm9aOebg%3D&reserved=0> > * > > * * > > ********************************************************** > > > > _______________________________________________ > > Gmod-ajax mailing list > > Gmo...@li... > > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > <https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fgmod-ajax&data=04%7C01%7Cjustin.elser%40oregonstate.edu%7C550a37b3ec78421a66ed08d99027fc9d%7Cce6d05e13c5e4d6287a84c4a2713c113%7C0%7C0%7C637699324131642281%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=h0lYBFA8r1bcF60LPwRd9NoZVlAJulTbXIzia9u%2FMN4%3D&reserved=0> > > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott at scottcain > dot net > GMOD Coordinator (http://gmod.org/ > <https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fgmod.org%2F&data=04%7C01%7Cjustin.elser%40oregonstate.edu%7C550a37b3ec78421a66ed08d99027fc9d%7Cce6d05e13c5e4d6287a84c4a2713c113%7C0%7C0%7C637699324131652232%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=F%2BqWqomOgT%2Bu2k0sf1NzajeL8EuSuTU1JZLmUS9aehc%3D&reserved=0>) > 216-392-3087 > Ontario Institute for Cancer Research > > > -- > ********************************************************** > * * > * Justin Elser * > * Computational Biology Post Doc * > * Dept. of Botany and Plant Pathology * > * Oregon State University * > * * > * email: el...@sc... * > * internet: www.science.oregonstate.edu/~elserj * > * * > ********************************************************** > > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > |
|
From: Justin E. <jus...@or...> - 2021-10-16 00:10:53
|
<html><head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
</head>
<body>
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 class="moz-cite-prefix">On 10/15/21 3:05 PM, Scott Cain wrote:<br>
</div>
<blockquote type="cite" cite="mid:CA+...@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">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..." 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..." 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%7C550a37b3ec78421a66ed08d99027fc9d%7Cce6d05e13c5e4d6287a84c4a2713c113%7C0%7C0%7C637699324131632320%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=QKpnruDgVGVi4knHL%2Feu8EgMcZ%2FimMJKFrWsm9aOebg%3D&reserved=0" originalsrc="http://www.science.oregonstate.edu/~elserj" shash="V+Xs8oXUGe37kfRMDmacfBHTBbkuaNdHLqy2rxIwralnd14kPPInmZVc+4pROHqbgRQX15VGMXnUmDlY2ZdTaqrBDqSG52Ljp+Ai1+Dd/n1JAZk4o2IqIyE93AbQ3rtwrcsdo0bUCH9d9t49bCGNTyfMlyCmjD6J/U4YK+MLg/c=" moz-do-not-send="true">www.science.oregonstate.edu/~elserj</a>
*<br>
> *
*<br>
>
**********************************************************<br>
><br>
> _______________________________________________<br>
> Gmod-ajax mailing list<br>
> <a href="mailto:Gmo...@li..." moz-do-not-send="true">Gmo...@li...</a><br>
> <a href="https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fgmod-ajax&data=04%7C01%7Cjustin.elser%40oregonstate.edu%7C550a37b3ec78421a66ed08d99027fc9d%7Cce6d05e13c5e4d6287a84c4a2713c113%7C0%7C0%7C637699324131642281%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=h0lYBFA8r1bcF60LPwRd9NoZVlAJulTbXIzia9u%2FMN4%3D&reserved=0" originalsrc="https://lists.sourceforge.net/lists/listinfo/gmod-ajax" shash="bPuAYZjhiaNpyTEbb7CXdF9hjiGn/0w1Oa3wXTWUaeJS6hEBgBNy1+VrVXGU7RdwTM1Qbyi1tPsgMYitkknsVOzgxeOeTrzY7k8TxCgecUVeC1bphWUmAPFbnpxyzm+5wOR1M3I9cmtKaopY9080+oXz++vcC6Q3lnMz2EV94Hk=" moz-do-not-send="true">https://lists.sourceforge.net/lists/listinfo/gmod-ajax</a><br>
<br>
<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%7C550a37b3ec78421a66ed08d99027fc9d%7Cce6d05e13c5e4d6287a84c4a2713c113%7C0%7C0%7C637699324131652232%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=F%2BqWqomOgT%2Bu2k0sf1NzajeL8EuSuTU1JZLmUS9aehc%3D&reserved=0" originalsrc="http://gmod.org/" shash="mdIre2V1CDFTVs9qwMd0o+K5YGfINL/8IiCHBAwbSGneyoU7A54nf6ctI5bA7vRIwYJpt68lpbggDFD5jNfBmF9u9On6KXPrtuCmEHwaXJk+P2/LcVH2kZvTohMWhVKOD8z8ExaGASODxuXlLJabm7cT7Cj2pAzCh3YgVNZQDIw=" moz-do-not-send="true">http://gmod.org/</a>)
216-392-3087<br>
Ontario Institute for Cancer Research</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>
</body>
</html>
|
|
From: Scott C. <sc...@sc...> - 2021-10-15 22:30:59
|
Hi Justin, 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? Scott On Fri, Oct 15, 2021 at 3:00 PM Justin Elser <jus...@or...> wrote: > > Hello, > > 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. > > 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: > > > I see this: > > > 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). > > 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". > > 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. > > 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. > > Also, just in case it helps, here are the relevant bits of the Apache vhost entries for both: > The one that works: > /etc/httpd/conf.d/salvia.conf > > Alias /jbrowse "/data/www/jbrowse/jbrowse" > > <Directory "/data/www/jbrowse/jbrowse"> > > AllowOverride All > > Require all granted > > </Directory> > > > The one that doesn't work: > /etc/httpd/conf.d/panoryza-ssl.conf > > Alias /jbrowse "/data/www/panoryza/jbrowse" > > <Directory "/data/www/panoryza/jbrowse"> > > AllowOverride All > > Require all granted > > </Directory> > > > > I would appreciate any help in figuring out what I am doing wrong or how to fix this. > > Thanks, > Justin Elser > > -- > ********************************************************** > * * > * Justin Elser * > * Computational Biology Post Doc * > * Dept. of Botany and Plant Pathology * > * Oregon State University * > * * > * email: el...@sc... * > * internet: www.science.oregonstate.edu/~elserj * > * * > ********************************************************** > > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research |
|
From: Justin E. <jus...@or...> - 2021-10-15 19:10:37
|
<html><head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
</head>
<body>
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>
<img src="cid:par...@or..." alt="" width="496" height="271"><br>
<br>
I see this:<br>
<img src="cid:par...@or..." alt="" width="876" height="264"><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>
<pre> Alias /jbrowse "/data/www/jbrowse/jbrowse"</pre>
<pre> <Directory "/data/www/jbrowse/jbrowse"></pre>
<pre> AllowOverride All</pre>
<pre> Require all granted</pre>
<pre> </Directory></pre>
<br>
The one that doesn't work:<br>
/etc/httpd/conf.d/panoryza-ssl.conf<br>
<pre> Alias /jbrowse "/data/www/panoryza/jbrowse"</pre>
<pre> <Directory "/data/www/panoryza/jbrowse"></pre>
<pre> AllowOverride All</pre>
<pre> Require all granted</pre>
<pre> </Directory></pre>
<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>
<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>
</body>
</html>
|
|
From: Charan T. <Cha...@eg...> - 2021-09-20 17:27:05
|
Hi,
All our "fa, fai, gff3, gz, etc..." files are in the AWS S3 bucket and we don't want to make our S3 bucket Public for security purposes.
I tried both GUI and CLI approaches for adding the files, I have doubts in both the approaches as follows:
Approach 1: GUI
While creating a new Genome Assembly, it is expecting only an URL , in our case even if I give the S3 URL, it won't be able to fetch it because S3's public access is blocked.
Is there an alternative way to create Genome Assembly without providing an URL, instead adding from the EC2 instance is preferred?
Approach 2: CLI
1. Can I add tracks without adding assembly?
2. I tried running " jbrowse add - track / data /*****.fa -- load copy" for adding tracks but I encountered -
" Error: ENOENT: no such file or directory, open './config.json'
Code: ENOENT
Try this:
* Make sure the file "./config.json" exists
* Run `jbrowse add-assembly` to create a config file
"
* If I have to run the 'jbrowse add-assembly /data/*****.fa --load copy' command, should I be in any specific directory to pick up the file? I am asking because when I run this command I am getting: " Error: Could not resolve to a file or a URL: " What am I missing here?
Please help me with detailed information.
--
Thanks,
Charan
Charan Thoomu
Software Engineer
eGenesis, Inc.
300 Technology Square, Suite 301
Cambridge, MA 02139
cha...@eg...<mailto:cha...@eg...>
www.egenesisbio.com<http://www.egenesisbio.com/>
|
|
From: Garrett S. <ste...@gm...> - 2021-09-20 16:58:17
|
Hi Charan, To answer one of your questions first, you cannot have tracks without an assembly. JBrowse needs the assembly to know what the chromosomes/contigs/etc. are that the tracks are being displayed on. As for your other questions, I'm not sure exactly what your setup is, so I'll try to explain what I can. You mention an EC2 instance, but then the screenshot you posted shows JBrowse being served locally. If you are hosting JBrowse on an EC2 instance, you can't currently use the GUI editor to add a local file. You'll have to do that with the CLI tool. Make sure you are running the CLI tool on your EC2 instance, not your local machine. You should probably run `jbrowse add-assembly` in the same directory you ran `jbrowse create` in, which should be somewhere in your web server (Apache, Nginx, etx.) directory (often that's "/var/www/html/", see this guide <https://jbrowse.org/jb2/docs/superquickstart_web/> for a quick example). Be aware that the command you posted will copy your .fa file into your web server directory, since it needs to be publicly served by the web server as well. Let me know if that helps, or if I'm misunderstanding your setup. Best, Garrett On Sun, Sep 19, 2021 at 1:56 AM Sunny Charan <cha...@gm...> wrote: > Hi Garrett, > > All our "fa, fai, gff3, gz, etc..." files are in the AWS S3 bucket and we > don't want to make our S3 bucket Public for security purposes. > > I tried both GUI and CLI approaches for adding the files, I have doubts in > both the approaches as follows: > > ####GUI Approach#### > While creating a new Genome Assembly, it is expecting only an URL , in our > case even if I give the S3 URL, it won't be able to fetch it because S3's > public access is blocked. > > Is there an alternative way to create Genome Assembly without providing an > URL, instead adding from the EC2 instance is preferred? > > [image: image.png] > > > ####CLI Approach#### > > 1. Can I add tracks without adding assembly? > 2. I tried running " jbrowse add - track / data /*****.fa -- load > copy" for adding tracks but I encountered - > > " Error: ENOENT: no such file or directory, open './config.json' > Code: ENOENT > Try this: > * Make sure the file "./config.json" exists > * Run `jbrowse add-assembly` to create a config file > " > > - If I have to run 'jbrowse add-assembly /data/*****.fa --load copy' > command, should I be in any specific directory to pick up the file? I am > asking because when I run this command I am getting: " Error: Could not > resolve to a file or a URL: " What am I missing here? > > Please help me with detailed information. > > > > On Mon, Aug 30, 2021 at 3:33 PM Garrett Stevens < > ste...@gm...> wrote: > >> Hi Charan, >> >> I'm not sure I understand what you are describing. Where are these error >> messages you see? Screenshots could help. Also, can you describe how you >> are adding the tracks (e.g. via CLI add-track, or admin-server, etc.)? >> >> JBrowse does support tabix-indexed GFF3 files (e.g. myfile.gff3.gz with >> myfile.gff3.gz.tbi), so it seems like the files you want to use would be >> supported. >> >> Also, make sure the bucket serving the files has the correct CORS >> configuration (see here >> <https://github.com/GMOD/jbrowse-components/discussions/2216> for more >> details). >> >> Best, >> Garrett >> >> On Mon, Aug 30, 2021 at 12:22 PM Sunny Charan <cha...@gm...> >> wrote: >> >>> Hi, >>> >>> I am in the process of setting up JBrowse 2 (1.3.5) on AWS EC2 instance. >>> >>> So far I installed the JBrowse 2 but when I was trying to "Add Tracks" >>> using the Object URL from S3 bucket which are in the .gff3 and .gz >>> extension. I see a prompt saying either one of the following: >>> >>> 1. Error: TypeError: NetworkError when attempting to fetch resources. >>> 2. This format is not supported by this version and is supported in >>> the latest version. I am reiterating again that I am using the latest >>> release 1.3.5. >>> >>> So, please help me further in doing the setup in a successful way where >>> I can upload the tracks without any issues. And also if there are any >>> specific file formats JBrowse 2 is supported which I am unaware of. >>> >>> -- >>> Thanks, >>> Charan >>> _______________________________________________ >>> Gmod-ajax mailing list >>> Gmo...@li... >>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >>> >> > > -- > Thanks, > Charan > |
|
From: Sunny C. <cha...@gm...> - 2021-09-19 07:58:32
|
Hi,
Hi Garrett,
All our "fa, fai, gff3, gz, etc..." files are in the AWS S3 bucket and we
don't want to make our S3 bucket Public for security purposes.
I tried both GUI and CLI approaches for adding the files, I have doubts in
both the approaches as follows:
####GUI Approach####
While creating a new Genome Assembly, it is expecting only an URL , in our
case even if I give the S3 URL, it won't be able to fetch it because S3's
public access is blocked.
Is there an alternative way to create Genome Assembly without providing an
URL, instead adding from the EC2 instance is preferred?
[image: image.png]
####CLI Approach####
1. Can I add tracks without adding assembly?
2. I tried running " jbrowse add - track / data /*****.fa -- load copy"
for adding tracks but I encountered -
" Error: ENOENT: no such file or directory, open './config.json'
Code: ENOENT
Try this:
* Make sure the file "./config.json" exists
* Run `jbrowse add-assembly` to create a config file
"
- If I have to run the 'jbrowse add-assembly /data/*****.fa --load copy'
command, should I be in any specific directory to pick up the file? I am
asking because when I run this command I am getting: " Error: Could not
resolve to a file or a URL: " What am I missing here?
Please help me with detailed information.
--
Thanks,
Charan
|
|
From: Sunny C. <cha...@gm...> - 2021-09-19 07:56:53
|
Hi Garrett,
All our "fa, fai, gff3, gz, etc..." files are in the AWS S3 bucket and we
don't want to make our S3 bucket Public for security purposes.
I tried both GUI and CLI approaches for adding the files, I have doubts in
both the approaches as follows:
####GUI Approach####
While creating a new Genome Assembly, it is expecting only an URL , in our
case even if I give the S3 URL, it won't be able to fetch it because S3's
public access is blocked.
Is there an alternative way to create Genome Assembly without providing an
URL, instead adding from the EC2 instance is preferred?
[image: image.png]
####CLI Approach####
1. Can I add tracks without adding assembly?
2. I tried running " jbrowse add - track / data /*****.fa -- load copy"
for adding tracks but I encountered -
" Error: ENOENT: no such file or directory, open './config.json'
Code: ENOENT
Try this:
* Make sure the file "./config.json" exists
* Run `jbrowse add-assembly` to create a config file
"
- If I have to run 'jbrowse add-assembly /data/*****.fa --load copy'
command, should I be in any specific directory to pick up the file? I am
asking because when I run this command I am getting: " Error: Could not
resolve to a file or a URL: " What am I missing here?
Please help me with detailed information.
On Mon, Aug 30, 2021 at 3:33 PM Garrett Stevens <ste...@gm...>
wrote:
> Hi Charan,
>
> I'm not sure I understand what you are describing. Where are these error
> messages you see? Screenshots could help. Also, can you describe how you
> are adding the tracks (e.g. via CLI add-track, or admin-server, etc.)?
>
> JBrowse does support tabix-indexed GFF3 files (e.g. myfile.gff3.gz with
> myfile.gff3.gz.tbi), so it seems like the files you want to use would be
> supported.
>
> Also, make sure the bucket serving the files has the correct CORS
> configuration (see here
> <https://github.com/GMOD/jbrowse-components/discussions/2216> for more
> details).
>
> Best,
> Garrett
>
> On Mon, Aug 30, 2021 at 12:22 PM Sunny Charan <cha...@gm...> wrote:
>
>> Hi,
>>
>> I am in the process of setting up JBrowse 2 (1.3.5) on AWS EC2 instance.
>>
>> So far I installed the JBrowse 2 but when I was trying to "Add Tracks"
>> using the Object URL from S3 bucket which are in the .gff3 and .gz
>> extension. I see a prompt saying either one of the following:
>>
>> 1. Error: TypeError: NetworkError when attempting to fetch resources.
>> 2. This format is not supported by this version and is supported in
>> the latest version. I am reiterating again that I am using the latest
>> release 1.3.5.
>>
>> So, please help me further in doing the setup in a successful way where I
>> can upload the tracks without any issues. And also if there are any
>> specific file formats JBrowse 2 is supported which I am unaware of.
>>
>> --
>> Thanks,
>> Charan
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>
--
Thanks,
Charan
|
|
From: Vaneet L. <van...@uc...> - 2021-09-13 16:06:33
|
Hello, Is there a way to show feature labels in collapsed displayMode? For a certain track that has many transcripts our group likes the way collapsed mode appears to shrink it down into one consensus gene model but of course since it's collapsed the feature labels are gone, anyway to leave them on? Also I noticed the option menu when you right click on the feature in normal mode is gone from collapsed mode, is there any way to bring that option back when it's collapsed so you can still right click on the feature to bring up those same options? Thanks, Vaneet Vaneet Lotay Xenbase Bioinformatician 716 ICT Building - University of Calgary 2500 University Drive NW Calgary, AB T2N 1N4 CANADA |
|
From: Cristina A. <au...@ug...> - 2021-09-12 20:28:15
|
Hi do you have a VPAT on accessibility for JBrowse, that describes its level of compliance to Section 508? Thanks Cristina ------ Cristina Aurrecoechea VEuPathDB UI Team |
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From: Vaneet L. <van...@uc...> - 2021-09-10 21:44:50
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Ok, that's what I thought, just checking. That is an interesting tool Biodalliance has, seems to be what we're trying to recreate...more or less. Thanks, Vaneet ________________________________ From: Colin <col...@gm...> Sent: September 10, 2021 2:45 PM To: Vaneet Lotay <van...@uc...> Cc: gmod-ajax <gmo...@li...> Subject: Re: [Gmod-ajax] Show labels in collapsed displayMode? [△EXTERNAL] >Thanks for those tips. Can you tell me how the collapsed mode works? For example, when there are multiple mRNA models in normal mode that collapse to one in collapsed mode, is it simply showing the longest possible transcript with the union of all possible exon and inner segments? It is not really doing anything intelligent, it simply plots all transcripts at y-coordinate 0. This is why in most cases, drawing labels and having mouseovers is a non-sense behavior in collapsed mode. The ChromHMM track is a nice special case where the collapsing gives a simple row of chromatin states though, so mouseovers and clicks are manually added via config There is perhaps a good need to make a smarter system. It is often overwhelming for every gene to have all transcript isoforms displayed all the time. Most people may be satisfied to show the union of possible exon/inner segments. Biodalliance has a mode kind of like this (the genes track when you visit here https://www.biodalliance.org/ has this enabled) -Colin On Fri, Sep 10, 2021 at 1:13 PM Vaneet Lotay <van...@uc...<mailto:van...@uc...>> wrote: Hey Colin, Thanks for those tips. Can you tell me how the collapsed mode works? For example, when there are multiple mRNA models in normal mode that collapse to one in collapsed mode, is it simply showing the longest possible transcript with the union of all possible exon and inner segments? Vaneet ________________________________ From: Colin <col...@gm...<mailto:col...@gm...>> Sent: September 9, 2021 4:34 PM To: Vaneet Lotay <van...@uc...<mailto:van...@uc...>> Cc: gmod-ajax <gmo...@li...<mailto:gmo...@li...>> Subject: Re: [Gmod-ajax] Show labels in collapsed displayMode? [△EXTERNAL] Also add disableCollapsedClick: false, See https://github.com/GMOD/jbrowse/blob/master/setup.sh#L208 for how this particular track is setup -Colin On Thu, Sep 9, 2021 at 6:30 PM Colin <col...@gm...<mailto:col...@gm...>> wrote: You can add a "enableCollapsedMouseover": true to get the right click on the collapsed tracks. The ChromHMM track in our volvox demo uses this https://jbrowse.org/code/JBrowse-1.16.11/?loc=ctgA%3A9881..32090&tracks=ChromHMM&data=sample_data%2Fjson%2Fvolvox&tracklist=1&highlight=&nav=1&overview=1 I am not sure we have feature labels in collapsed mode but there is a mouseover -Colin On Thu, Sep 9, 2021 at 4:35 PM Vaneet Lotay <van...@uc...<mailto:van...@uc...>> wrote: Hello, Is there a way to show feature labels in collapsed displayMode? For a certain track that has many transcripts our group likes the way collapsed mode appears to shrink it down into one consensus gene model but of course since it’s collapsed the feature labels are gone, anyway to leave them on? Also I noticed the option menu when you right click on the feature in normal mode is gone from collapsed mode, is there any way to bring that option back when it’s collapsed so you can still right click on the feature to bring up those same options? Thanks, Vaneet Vaneet Lotay Xenbase Bioinformatician 716 ICT Building – University of Calgary 2500 University Drive NW Calgary, AB T2N 1N4 CANADA _______________________________________________ Gmod-ajax mailing list Gmo...@li...<mailto:Gmo...@li...> https://lists.sourceforge.net/lists/listinfo/gmod-ajax |
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From: Colin <col...@gm...> - 2021-09-10 20:45:49
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>Thanks for those tips. Can you tell me how the collapsed mode works? For example, when there are multiple mRNA models in normal mode that collapse to one in collapsed mode, is it simply showing the longest possible transcript with the union of all possible exon and inner segments? It is not really doing anything intelligent, it simply plots all transcripts at y-coordinate 0. This is why in most cases, drawing labels and having mouseovers is a non-sense behavior in collapsed mode. The ChromHMM track is a nice special case where the collapsing gives a simple row of chromatin states though, so mouseovers and clicks are manually added via config There is perhaps a good need to make a smarter system. It is often overwhelming for every gene to have all transcript isoforms displayed all the time. Most people may be satisfied to show the union of possible exon/inner segments. Biodalliance has a mode kind of like this (the genes track when you visit here https://www.biodalliance.org/ has this enabled) -Colin On Fri, Sep 10, 2021 at 1:13 PM Vaneet Lotay <van...@uc...> wrote: > Hey Colin, > > Thanks for those tips. Can you tell me how the collapsed mode works? For > example, when there are multiple mRNA models in normal mode that collapse > to one in collapsed mode, is it simply showing the longest possible > transcript with the union of all possible exon and inner segments? > > Vaneet > ------------------------------ > *From:* Colin <col...@gm...> > *Sent:* September 9, 2021 4:34 PM > *To:* Vaneet Lotay <van...@uc...> > *Cc:* gmod-ajax <gmo...@li...> > *Subject:* Re: [Gmod-ajax] Show labels in collapsed displayMode? > > [△EXTERNAL] > > Also add > > disableCollapsedClick: false, > > See https://github.com/GMOD/jbrowse/blob/master/setup.sh#L208 > > for how this particular track is setup > > -Colin > > On Thu, Sep 9, 2021 at 6:30 PM Colin <col...@gm...> wrote: > > You can add a "enableCollapsedMouseover": true to get the right click on > the collapsed tracks. The ChromHMM track in our volvox demo uses this > > > https://jbrowse.org/code/JBrowse-1.16.11/?loc=ctgA%3A9881..32090&tracks=ChromHMM&data=sample_data%2Fjson%2Fvolvox&tracklist=1&highlight=&nav=1&overview=1 > > I am not sure we have feature labels in collapsed mode but there is a > mouseover > > > -Colin > > On Thu, Sep 9, 2021 at 4:35 PM Vaneet Lotay <van...@uc...> > wrote: > > Hello, > > > > Is there a way to show feature labels in collapsed displayMode? For a > certain track that has many transcripts our group likes the way collapsed > mode appears to shrink it down into one consensus gene model but of course > since it’s collapsed the feature labels are gone, anyway to leave them on? > Also I noticed the option menu when you right click on the feature in > normal mode is gone from collapsed mode, is there any way to bring that > option back when it’s collapsed so you can still right click on the feature > to bring up those same options? > > > > Thanks, > > > > Vaneet > > > > *Vaneet Lotay* > > *Xenbase Bioinformatician* > > *716 ICT Building – University of Calgary* > > *2500 University Drive NW* > > *Calgary, AB T2N 1N4* > > *CANADA* > > > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > > |
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From: Vaneet L. <van...@uc...> - 2021-09-10 17:13:52
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Hey Colin,
Thanks for those tips. Can you tell me how the collapsed mode works? For example, when there are multiple mRNA models in normal mode that collapse to one in collapsed mode, is it simply showing the longest possible transcript with the union of all possible exon and inner segments?
Vaneet
________________________________
From: Colin <col...@gm...>
Sent: September 9, 2021 4:34 PM
To: Vaneet Lotay <van...@uc...>
Cc: gmod-ajax <gmo...@li...>
Subject: Re: [Gmod-ajax] Show labels in collapsed displayMode?
[△EXTERNAL]
Also add
disableCollapsedClick: false,
See https://github.com/GMOD/jbrowse/blob/master/setup.sh#L208
for how this particular track is setup
-Colin
On Thu, Sep 9, 2021 at 6:30 PM Colin <col...@gm...<mailto:col...@gm...>> wrote:
You can add a "enableCollapsedMouseover": true to get the right click on the collapsed tracks. The ChromHMM track in our volvox demo uses this
https://jbrowse.org/code/JBrowse-1.16.11/?loc=ctgA%3A9881..32090&tracks=ChromHMM&data=sample_data%2Fjson%2Fvolvox&tracklist=1&highlight=&nav=1&overview=1
I am not sure we have feature labels in collapsed mode but there is a mouseover
-Colin
On Thu, Sep 9, 2021 at 4:35 PM Vaneet Lotay <van...@uc...<mailto:van...@uc...>> wrote:
Hello,
Is there a way to show feature labels in collapsed displayMode? For a certain track that has many transcripts our group likes the way collapsed mode appears to shrink it down into one consensus gene model but of course since it’s collapsed the feature labels are gone, anyway to leave them on? Also I noticed the option menu when you right click on the feature in normal mode is gone from collapsed mode, is there any way to bring that option back when it’s collapsed so you can still right click on the feature to bring up those same options?
Thanks,
Vaneet
Vaneet Lotay
Xenbase Bioinformatician
716 ICT Building – University of Calgary
2500 University Drive NW
Calgary, AB T2N 1N4
CANADA
_______________________________________________
Gmod-ajax mailing list
Gmo...@li...<mailto:Gmo...@li...>
https://lists.sourceforge.net/lists/listinfo/gmod-ajax
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From: Colin <col...@gm...> - 2021-09-09 22:35:02
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Also add
disableCollapsedClick: false,
See https://github.com/GMOD/jbrowse/blob/master/setup.sh#L208
for how this particular track is setup
-Colin
On Thu, Sep 9, 2021 at 6:30 PM Colin <col...@gm...> wrote:
> You can add a "enableCollapsedMouseover": true to get the right click on
> the collapsed tracks. The ChromHMM track in our volvox demo uses this
>
>
> https://jbrowse.org/code/JBrowse-1.16.11/?loc=ctgA%3A9881..32090&tracks=ChromHMM&data=sample_data%2Fjson%2Fvolvox&tracklist=1&highlight=&nav=1&overview=1
>
> I am not sure we have feature labels in collapsed mode but there is a
> mouseover
>
>
> -Colin
>
> On Thu, Sep 9, 2021 at 4:35 PM Vaneet Lotay <van...@uc...>
> wrote:
>
>> Hello,
>>
>>
>>
>> Is there a way to show feature labels in collapsed displayMode? For a
>> certain track that has many transcripts our group likes the way collapsed
>> mode appears to shrink it down into one consensus gene model but of course
>> since it’s collapsed the feature labels are gone, anyway to leave them on?
>> Also I noticed the option menu when you right click on the feature in
>> normal mode is gone from collapsed mode, is there any way to bring that
>> option back when it’s collapsed so you can still right click on the feature
>> to bring up those same options?
>>
>>
>>
>> Thanks,
>>
>>
>>
>> Vaneet
>>
>>
>>
>> *Vaneet Lotay*
>>
>> *Xenbase Bioinformatician*
>>
>> *716 ICT Building – University of Calgary*
>>
>> *2500 University Drive NW*
>>
>> *Calgary, AB T2N 1N4*
>>
>> *CANADA*
>>
>>
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>
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From: Colin <col...@gm...> - 2021-09-09 22:30:42
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You can add a "enableCollapsedMouseover": true to get the right click on the collapsed tracks. The ChromHMM track in our volvox demo uses this https://jbrowse.org/code/JBrowse-1.16.11/?loc=ctgA%3A9881..32090&tracks=ChromHMM&data=sample_data%2Fjson%2Fvolvox&tracklist=1&highlight=&nav=1&overview=1 I am not sure we have feature labels in collapsed mode but there is a mouseover -Colin On Thu, Sep 9, 2021 at 4:35 PM Vaneet Lotay <van...@uc...> wrote: > Hello, > > > > Is there a way to show feature labels in collapsed displayMode? For a > certain track that has many transcripts our group likes the way collapsed > mode appears to shrink it down into one consensus gene model but of course > since it’s collapsed the feature labels are gone, anyway to leave them on? > Also I noticed the option menu when you right click on the feature in > normal mode is gone from collapsed mode, is there any way to bring that > option back when it’s collapsed so you can still right click on the feature > to bring up those same options? > > > > Thanks, > > > > Vaneet > > > > *Vaneet Lotay* > > *Xenbase Bioinformatician* > > *716 ICT Building – University of Calgary* > > *2500 University Drive NW* > > *Calgary, AB T2N 1N4* > > *CANADA* > > > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > |
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From: Vaneet L. <van...@uc...> - 2021-09-09 20:34:39
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Hello, Is there a way to show feature labels in collapsed displayMode? For a certain track that has many transcripts our group likes the way collapsed mode appears to shrink it down into one consensus gene model but of course since it's collapsed the feature labels are gone, anyway to leave them on? Also I noticed the option menu when you right click on the feature in normal mode is gone from collapsed mode, is there any way to bring that option back when it's collapsed so you can still right click on the feature to bring up those same options? Thanks, Vaneet Vaneet Lotay Xenbase Bioinformatician 716 ICT Building - University of Calgary 2500 University Drive NW Calgary, AB T2N 1N4 CANADA |
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From: Colin <col...@gm...> - 2021-09-02 21:32:46
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Hi, glad to hear from you Ke :) Currently this feature is tracked in this feature request. https://github.com/GMOD/jbrowse-components/issues/463 It is not currently prioritized but I think a lot of people would like it! There is a github function to subscribe to the issue if you want updates. If you have any interest in developing the features let me know too...could try to create an outline for what is needed. -Colin On Thu, Sep 2, 2021 at 3:41 PM Ke Jiang <bio...@gm...> wrote: > Hi, > > One feature I kind of miss from JBrowse was when zooming out a feature > track (such as genes or repetitive elements) would condense and binned into > a histogram. Is there a plan to implement this in JBrowse2? Sometimes this > function could be handy to show chromosome-wide information and seems > available from other genome browsers. > > Thanks! > > Ke > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > |
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From: Ke J. <bio...@gm...> - 2021-09-02 19:41:07
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Hi, One feature I kind of miss from JBrowse was when zooming out a feature track (such as genes or repetitive elements) would condense and binned into a histogram. Is there a plan to implement this in JBrowse2? Sometimes this function could be handy to show chromosome-wide information and seems available from other genome browsers. Thanks! Ke |
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From: Timothy F. <tf...@uc...> - 2021-09-01 20:15:15
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Hello Apollo <https://github.com/GMOD/Apollo> users (and CCed JBrowse2 user list), I tried Apollo some years ago, but it didn’t quite work for my genome annotation problem (my memory is a little fuzzy as to why it didn’t work out). I’d like to give it another shot, but have a couple questions that I think your respective user communities might have insight into: 1. Does Apollo’s graphical editing of gene models have a mode where it biologically constrains the edits? E.g. exon-intron splice junctions can only be dragged to another valid slide junction (based the AG/GT sites), or start codons can only be dragged to other ATGs (in other words, these features would “snap” to coordinates that have compatible sequences with their biological function) 2. Does anyone have a favored strategy or suite of tools for manual or semi-automated gene family annotation? In my past work, I came down on the “mostly-manual” side of things - looking at blast alignments in a genome browser, manually editing the GFF file with nano, and regenerating the translated peptides from the GFF to make sure I didn’t muck up the splicing or frame, while tracking it all with git to ensure I had a sort of “audit log” for these changes as I did them on-and-off over a few weeks. You can actually see the history of that here: https://github.com/photocyte/PPYR_OGS/commits/master <https://github.com/photocyte/PPYR_OGS/commits/master> . I’m sure there must be a better way to do things (and Apollo may be it!) but I hadn’t quite figured it out yet. I greatly appreciate any guidance you can provide. All the best, -Tim ___________________________________ Timothy R. Fallon, PhD NIH NRSA Postdoctoral Fellow - Moore Laboratory Center for Marine Biotechnology and Biomedicine Scripps Institution of Oceanography University of California, San Diego tf...@uc... Google Scholar publications and citations <https://scholar.google.com/citations?hl=en&user=CEPlauQAAAAJ&view_op=list_works&sortby=pubdate> Website: http://photocyte.github.io <http://photocyte.github.io/> |
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