gmod-ajax — JBrowse list

[Gmod-ajax] request for support

[Onkar N. <onk...@gm...>]

Dear JBrowse team,
I want to imbed JBrowse into my html page. So I tried installing it on my
system. But I am getting an error of zlib.h. I have tried the instructions
available on your wikipage and some others by google search. But none has
worked. Kindly Consider the related log file.
Any support will be helpful.
Waiting eagerly for your reply.

Regards
--

ONKAR NATH
Senior Research Fellow
National Institute of Plant Genome Research
Aruna Asaf Ali Marg, New Delhi- 110067
Email- onk...@gm...
Mob: +91-9136065766
skype id: onkarnath89

Re: [Gmod-ajax] JBrowse error in BAM file

[Colin <col...@gm...>]

There are a couple things going on. If there is a 404, then it seems it is
somehow literally not pointing to the right file. For example it seems like
the 404 is for /jbrowse/bams/mybam.bam.bai instead of from the data folder,
presumably at /jbrowse/data/mybam.bam.bai. You can maybe edit the
data/trackList.json file and see where it is pointing to, and email the
contents of the trackList if you need guidance?


Then further the problem about "Not a BAM" is a problem too. CentOS/RedHat
is sort of notorious for this particular issue, but it is documented how to
solve and you did the right thing with the AddType configuration addition.
I guess I would just check that this Apache configuration change that you
made was enabled properly

There is a FAQ entry here about it
http://gmod.org/wiki/JBrowse_FAQ#How_do_I_fix_the_.22Not_a_BAM_file.22_issue.3F

Hope that helps!

-Colin


On Tue, Jun 12, 2018 at 11:16 PM Changfa Yin <yin...@ca...> wrote:

> Hi,
> I tried "add-bam-track.pl --label mybam --bam_url mybam.bam --in
> data/trackList.json"
> but not jbrowse work with the warning of:
> 404 (Not Found) when attempting to fetch:
> httpd://localhost/jbrowse/bams/mybam.bam.bai
>
> but the mybam.bam.bai file existed there.
>
> I have add the line below into the httpd.conf:
> AddType application/octet-stream .bam .bami .bai
> but the volvox test file also shows the bug of "Not a BAM".
>
> $ lsb_release -a
> LSB Version:
> :base-4.0-amd64:base-4.0-noarch:core-4.0-amd64:core-4.0-noarch:graphics-4.0-amd64:graphics-4.0-noarch:printing-4.0-amd64:printing-4.0-noarch
> Distributor ID: CentOS
> Description:    CentOS release 6.8 (Final)
> Release:        6.8
> Codename:       Final
>
> Thank you !
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] JBrowse error in BAM file

[Changfa Y. <yin...@ca...>]

Hi,
I tried "add-bam-track.pl --label mybam --bam_url mybam.bam --in data/trackList.json"
but not jbrowse work with the warning of:
404 (Not Found) when attempting to fetch:
httpd://localhost/jbrowse/bams/mybam.bam.bai

but the mybam.bam.bai file existed there.

I have add the line below into the httpd.conf:
AddType application/octet-stream .bam .bami .bai
but the volvox test file also shows the bug of "Not a BAM".

$ lsb_release -a
LSB Version:	:base-4.0-amd64:base-4.0-noarch:core-4.0-amd64:core-4.0-noarch:graphics-4.0-amd64:graphics-4.0-noarch:printing-4.0-amd64:printing-4.0-noarch
Distributor ID:	CentOS
Description:	CentOS release 6.8 (Final)
Release:	6.8
Codename:	Final

Thank you !

[Gmod-ajax] requesting CRAM test data

[Robert B. <rb...@gm...>]

Hi all,

I'm working right now on adding support for opening CRAM files. I'd like to
gather some more test data to make sure it works well with as many
different kinds of CRAM files as possible, since CRAM is a very complex
format with support for a lot of different compression techniques, not all
of which are used by every producer of CRAM files.

So if you have CRAM files that you can share, would you mind emailing me
directly with a download link to each CRAM file and its reference genome
file(s), and what tool and version produced the file?

This will help ensure that when JBrowse 1.15 comes out with CRAM support,
it will work with your CRAM files.  :-)

Thanks in advance!

Rob

Re: [Gmod-ajax] FW: Plugins not working with JBrowse-1.14.1-dev

[Robert B. <rb...@gm...>]

It looks to me like the plugin authors need to update their CSS for the
newest JBrowse. Perhaps try contacting them again?

If they are really not interested, if I were you I would fork it on GitHub
and fix it for my needs, then submit a pull request back to them.
On Tue, Jun 5, 2018 at 1:26 PM Vaneet Lotay <van...@uc...>
wrote:

> Hey guys,
>
>
>
> Do you have any thoughts yet on how else I can resolve the issues (below
> in previous e-mail) with the ComboTrackSelector plugin (
> https://github.com/Arabidopsis-Information-Portal/ComboTrackSelector)
>
>
>
> I’ve attached the browser console messages when I try to load the plugin.
>
>
>
> I tried contacting the developers of the plugin but have not got a
> response back yet.
>
>
>
> The plugin seems to function fine, but it’s purely an issue with the way
> it looks and how it’s placed in the tracklist pane, if you view the
> screenshot.
>
>
>
> Again this plugin is working in the current version of JBrowse that I have
> (JBrowse 1.13.1-dev), but when I try to upgrade to the newer versions and
> run the setup scripts I get the result in the screenshot attached.
>
>
>
> Would appreciate any help or suggestions.
>
>
>
> Thanks,
>
>
>
> Vaneet
>
>
>
> *Vaneet Lotay*
>
> *Xenbase Bioinformatician*
>
> *716 ICT Building - University of Calgary*
>
> *2500 University Drive NW*
>
> *Calgary AB T2N 1N4*
>
> *CANADA*
>
>
>
> *From:* Vaneet Lotay [mailto:van...@uc...]
> *Sent:* Monday, May 07, 2018 1:38 PM
> *To:* 'Colin' <col...@gm...>; 'Robert Buels' <rb...@gm...>
> *Cc:* 'gmo...@li...' <gmo...@li...>
>
>
> *Subject:* Re: [Gmod-ajax] Plugins not working with JBrowse-1.14.1-dev
>
>
>
> Thanks Colin.  The latest release of the multibigwig repo fixed that bug.
>
>
>
> I’m still having problems with the ComboTrackSelector plugin though, it
> loads fine but it draws the button for Faceted Track Selector over top of
> the Hierarchical track selector (screenshot attached of my example).
>
>
>
> This is what the browser console printed when I accessed a genome using
> ComboTrackSelector:
>
>
>
> Loaded ComboTrackSelector plugin
>
> /JBrowse-1.14.1-dev/dist/0.bundle.js:41819 plugin HideTracksButton
> constructor
>
> /JBrowse-1.14.1-dev/dist/0.bundle.js:41928 FeatureSequence plugin
> initialized.
>
> /JBrowse-1.14.1-dev/dist/0.bundle.js:647 In JBrowse configuration,
> datasets specified, but dataset_id not set.  Dataset selector will not be
> shown.
>
> (anonymous) @ /JBrowse-1.14.1-dev/dist/0.bundle.js:647
>
> www.google-analytics.com/analytics.js Failed to load resource:
> net::ERR_BLOCKED_BY_CLIENT
>
> circleIcon.png Failed to load resource: the server responded with a status
> of 404 (Not Found)
>
>
>
> I believe the warning in yellow is okay, I don’t want a dataset selector
> for this data directory, it’s a test space for me, mainly testing this
> plugin.
>
>
>
> Please let me know if there’s anything I can fix to make the plugin work.
>
>
> Vaneet
>
>
>
> *Vaneet Lotay*
>
> *Xenbase Bioinformatician*
>
> *716 ICT Building - University of Calgary*
>
> *2500 University Drive NW*
>
> *Calgary AB T2N 1N4*
>
> *CANADA*
>
>
>
> *From:* Colin [mailto:col...@gm... <col...@gm...>]
> *Sent:* Friday, May 04, 2018 6:46 PM
> *To:* Robert Buels <rb...@gm...>
> *Cc:* gmo...@li...
> *Subject:* Re: [Gmod-ajax] Plugins not working with JBrowse-1.14.1-dev
>
>
>
> With multibigwig at least, there was a bugfix added to support 1.14.1,
> should be able to pull this from multibigwig's GitHub repo and rerun setup
>
>
>
> -Colin
>
>
>
> On Fri, May 4, 2018, 8:14 PM Robert Buels <rb...@gm...> wrote:
>
> Are any errors shown in the browser’s developer console?
>
> On Fri, May 4, 2018 at 1:22 PM Nathan Dunn <nat...@lb...> wrote:
>
>
>
> You may want to open GitHub issues for the original plugins, as well.
>
>
>
> GH pointers from here: https://gmod.github.io/jbrowse-registry/
>
>
>
> Nathan
>
>
>
>
>
> On May 4, 2018, at 1:14 PM, Vaneet Lotay <van...@uc...> wrote:
>
>
>
> Hello,
>
>
>
> I currently have JBrowse-1.13.1-dev installed, was looking to upgrade to
> version JBrowse-1.14-1-dev.  When I was testing the new version I noticed 2
> of my additional plugins not working:
>
>
>
> ComboTrackSelector
> MultiBigWig
>
>
>
> For the ComboTrackSelector plugin it still allows me to select the Faceted
> Track Selector, but it seems to place it right over the tracklist pane,
> that is it blocks the tracks on the Hierarchical track selector.  Whereas
> when the plugin is working properly it moves the tracks in the tracklist
> down to allow space for the click in button for the Faceted track selector.
>
>
>
> For the MultiBigWig plugin I can see the track I produced via the
> MultiBigWig plugin but nothing is graphed on the track, no plot is drawn, I
> just see the track label.
>
>
>
> This was all after I ran the setup.sh script and the ‘npm run build’
> command by the way.
>
>
>
> Thanks,
>
>
>
> Vaneet
>
>
>
>
>
> *Vaneet Lotay*
>
> *Xenbase Bioinformatician*
>
> *716 ICT Building - University of Calgary*
>
> *2500 University Drive NW*
>
> *Calgary AB T2N 1N4*
>
> *CANADA*
>
>
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org <http://slashdot.org/>!
> http://sdm.link/slashdot_______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
>
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
>

[Gmod-ajax] FW: Plugins not working with JBrowse-1.14.1-dev

[Vaneet L. <van...@uc...>]

Hey guys,

Do you have any thoughts yet on how else I can resolve the issues (below in previous e-mail) with the ComboTrackSelector plugin (https://github.com/Arabidopsis-Information-Portal/ComboTrackSelector)

I've attached the browser console messages when I try to load the plugin.

I tried contacting the developers of the plugin but have not got a response back yet.

The plugin seems to function fine, but it's purely an issue with the way it looks and how it's placed in the tracklist pane, if you view the screenshot.

Again this plugin is working in the current version of JBrowse that I have (JBrowse 1.13.1-dev), but when I try to upgrade to the newer versions and run the setup scripts I get the result in the screenshot attached.

Would appreciate any help or suggestions.

Thanks,

Vaneet


Vaneet Lotay

Xenbase Bioinformatician

716 ICT Building - University of Calgary

2500 University Drive NW

Calgary AB T2N 1N4

CANADA

From: Vaneet Lotay [mailto:van...@uc...]
Sent: Monday, May 07, 2018 1:38 PM
To: 'Colin' <col...@gm...>; 'Robert Buels' <rb...@gm...>
Cc: 'gmo...@li...' <gmo...@li...>
Subject: Re: [Gmod-ajax] Plugins not working with JBrowse-1.14.1-dev

Thanks Colin.  The latest release of the multibigwig repo fixed that bug.

I'm still having problems with the ComboTrackSelector plugin though, it loads fine but it draws the button for Faceted Track Selector over top of the Hierarchical track selector (screenshot attached of my example).

This is what the browser console printed when I accessed a genome using ComboTrackSelector:

Loaded ComboTrackSelector plugin
/JBrowse-1.14.1-dev/dist/0.bundle.js:41819 plugin HideTracksButton constructor
/JBrowse-1.14.1-dev/dist/0.bundle.js:41928 FeatureSequence plugin initialized.
/JBrowse-1.14.1-dev/dist/0.bundle.js:647 In JBrowse configuration, datasets specified, but dataset_id not set.  Dataset selector will not be shown.
(anonymous) @ /JBrowse-1.14.1-dev/dist/0.bundle.js:647
www.google-analytics.com/analytics.js<http://www.google-analytics.com/analytics.js> Failed to load resource: net::ERR_BLOCKED_BY_CLIENT
circleIcon.png Failed to load resource: the server responded with a status of 404 (Not Found)

I believe the warning in yellow is okay, I don't want a dataset selector for this data directory, it's a test space for me, mainly testing this plugin.

Please let me know if there's anything I can fix to make the plugin work.

Vaneet

Vaneet Lotay
Xenbase Bioinformatician
716 ICT Building - University of Calgary
2500 University Drive NW
Calgary AB T2N 1N4
CANADA

From: Colin [mailto:col...@gm...]
Sent: Friday, May 04, 2018 6:46 PM
To: Robert Buels <rb...@gm...<mailto:rb...@gm...>>
Cc: gmo...@li...<mailto:gmo...@li...>
Subject: Re: [Gmod-ajax] Plugins not working with JBrowse-1.14.1-dev

With multibigwig at least, there was a bugfix added to support 1.14.1, should be able to pull this from multibigwig's GitHub repo and rerun setup

-Colin

On Fri, May 4, 2018, 8:14 PM Robert Buels <rb...@gm...<mailto:rb...@gm...>> wrote:
Are any errors shown in the browser's developer console?
On Fri, May 4, 2018 at 1:22 PM Nathan Dunn <nat...@lb...<mailto:nat...@lb...>> wrote:

You may want to open GitHub issues for the original plugins, as well.

GH pointers from here: https://gmod.github.io/jbrowse-registry/

Nathan


On May 4, 2018, at 1:14 PM, Vaneet Lotay <van...@uc...<mailto:van...@uc...>> wrote:

Hello,

I currently have JBrowse-1.13.1-dev installed, was looking to upgrade to version JBrowse-1.14-1-dev.  When I was testing the new version I noticed 2 of my additional plugins not working:

ComboTrackSelector
MultiBigWig

For the ComboTrackSelector plugin it still allows me to select the Faceted Track Selector, but it seems to place it right over the tracklist pane, that is it blocks the tracks on the Hierarchical track selector.  Whereas when the plugin is working properly it moves the tracks in the tracklist down to allow space for the click in button for the Faceted track selector.

For the MultiBigWig plugin I can see the track I produced via the MultiBigWig plugin but nothing is graphed on the track, no plot is drawn, I just see the track label.

This was all after I ran the setup.sh script and the 'npm run build' command by the way.

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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[Gmod-ajax] JBrowse 1.14.2 released

[Robert B. <rb...@gm...>]

Hello all,

JBrowse 1.14.2 has been released!

Files for download

   - JBrowse-1.14.2.zip
   <https://github.com/GMOD/jbrowse/releases/download/1.14.2-release/JBrowse-1.14.2.zip>
–
   2.8M
   file SHA1 77c28aa4e00b93b1f1e72c5071aee77e7eaa7baa
   - JBrowse-1.14.2-dev.zip
   <https://github.com/GMOD/jbrowse/releases/download/1.14.2-release/JBrowse-1.14.2-dev.zip>
–
   7.5M
   file SHA1 63b8e0bd8f3ae1f67e6a2e88ce514507a2e756d9

Minor improvements

   -

   Added a datasetSelectorWidth configuration key that sets the width of
   the dataset
   selector. The width defaults to 15em. Example setting in tracks.conf:

   [GENERAL]
   classicMenu = true
   datasetSelectorWidth = 20em

   Thanks to @srobb1 <https://github.com/srobb1> for pointing out the need
   for this. (issue #1059 <https://github.com/gmod/jbrowse/issues/1059>,
   @rbuels <https://github.com/rbuels>)
   -

   When exporting GFF3 from the ‘Save track data’ menu, the
   ##sequence-region pragma now
   specifies the exact sequence region that was exported from the UI.
   Thanks to @mwdavis2 <https://github.com/mwdavis2>
   for pointing this out! (issue #905
   <https://github.com/gmod/jbrowse/issues/905>, @rbuels
   <https://github.com/rbuels>)
   -

   Improved the welcome screen for the desktop version of JBrowse
   (issue #1045 <https://github.com/gmod/jbrowse/issues/1045>, issue #1050
   <https://github.com/gmod/jbrowse/pull/1050>, @cmdcolin
   <https://github.com/cmdcolin>)

Bug fixes

   -

   Fixed the --config option for add-bw-track.pl. Although documented in
   the script’s POD,
   it was not actually being processed. Thanks to @loraine-gueguen
   <https://github.com/loraine-gueguen> for noticing it, and for
   contributing the fix! (issue #1063
   <https://github.com/gmod/jbrowse/issues/1063>, issue #1064
   <https://github.com/gmod/jbrowse/pull/1064>, @loraine-gueguen
   <https://github.com/loraine-gueguen>)
   -

   Fixed a bug in which setup.sh failed if run twice in a row under some
   circumstances.
   (issue #1053 <https://github.com/gmod/jbrowse/pull/1053>, @cmdcolin
   <https://github.com/cmdcolin>)
   -

   Fixed a bug in which setup.sh did not accept nodejs version 10 as
   sufficiently recent.
   (issue #1048 <https://github.com/gmod/jbrowse/pull/1048>, @cmdcolin
   <https://github.com/cmdcolin>)
   -

   Fixed a bug in which the “Loading…” message erroneously appeared at the
   top of the
   dataset-selection page. Many thanks to @srobb1
   <https://github.com/srobb1> for noticing this and reporting it!
   (issue #1057 <https://github.com/gmod/jbrowse/issues/1057>, @rbuels
   <https://github.com/rbuels>)
   -

   JSON syntax errors in the new configuration loading code now have better
   error messages.
   Thanks to @billzt <https://github.com/billzt> for pointing out the need
   for this! (issue #1061 <https://github.com/gmod/jbrowse/issues/1061>,
   @rbuels <https://github.com/rbuels>)

Re: [Gmod-ajax] [apollo] Automated Screenshots

[Keiran R. <kr...@sa...>]

Hi all,

We've had something for a while which was PhantomJS but we've now updated to Puppeteer as it handles loading of more network heavy tracks better ensuring everything loads without the need for arbitrary waits.

It's specifically designed to allow many screen shots using a BED file for locations, the base URL can be changed within the run too:

https://github.com/cancerit/cgpJBrowseToolkit#jbrowse_rasterize

Regards,

Keiran Raine, M.Sc., MBCS
Principal Bioinformatician
Cancer, Ageing and Somatic Mutation
Wellcome Sanger Institute

kr...@sa...
Tel:+44 (0)1223 834244 Ext: 4983
Office: H104

Please note that due to childcare I don't work from 14:00 on Tuesdays and 14:50 on Wednesdays.

From: Nathan Dunn <nat...@lb...>
Date: Wednesday, 9 May 2018 at 18:38
To: Apollo List <ap...@li...>, gmod-ajax <gmo...@li...>
Subject: Re: [Gmod-ajax] [apollo] Automated Screenshots


That sounds fascinating!

I’m cross-posting to the gmod-ajax list.  I think the easiest solution might be to integrate a JBrowse plugin that does this out of the box such as this one:

https://github.com/bhofmei/jbplugin-screenshot


I’ve also run the Manet npm server: https://www.npmjs.com/package/manet against JBrowse / Apollo URLs to create screenshots.

Nathan



On May 9, 2018, at 10:30 AM, Abhijit Sanyal <abh...@gm...<mailto:abh...@gm...>> wrote:

Hi Nathan,

I want to capture screenshots around particular reference genes (gene and flanking 5 kb) in a way that I can see all the tracks with evidences for that gene in one screenshot. Purpose is to do some image analytics

-Abhijit

On Wed, May 9, 2018 at 10:22 PM, Nathan Dunn <nat...@lb...<mailto:nat...@lb...>> wrote:
Abhijit,

There are quite a few options.

What is the purpose of the screen shots?

Nathan

> On May 9, 2018, at 9:50 AM, Abhijit Sanyal <abh...@gm...<mailto:abh...@gm...>> wrote:
>
> Hello,
>
> I was wondering whether there was some script/module that one could run, on the command line, to capture screenshots in an automated fashion from Apollo. Using screen capture is too cumbersome since I have a lot of image captures to do.
>
> Thanks
> Abhijit
>
>
>
> This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
> If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to sy...@li...<mailto:sy...@li...> | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.
>





This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to sy...@li...<mailto:sy...@li...> | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.





This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to sy...@li...<mailto:sy...@li...> | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.





-- 
 The Wellcome Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE.

Re: [Gmod-ajax] [apollo] Automated Screenshots

[Nathan D. <nat...@lb...>]

That sounds fascinating! 

I’m cross-posting to the gmod-ajax list.  I think the easiest solution might be to integrate a JBrowse plugin that does this out of the box such as this one:

https://github.com/bhofmei/jbplugin-screenshot <https://github.com/bhofmei/jbplugin-screenshot>


I’ve also run the Manet npm server: https://www.npmjs.com/package/manet <https://www.npmjs.com/package/manet> against JBrowse / Apollo URLs to create screenshots.  

Nathan


> On May 9, 2018, at 10:30 AM, Abhijit Sanyal <abh...@gm...> wrote:
> 
> Hi Nathan,
> 
> I want to capture screenshots around particular reference genes (gene and flanking 5 kb) in a way that I can see all the tracks with evidences for that gene in one screenshot. Purpose is to do some image analytics
> 
> -Abhijit
> 
> On Wed, May 9, 2018 at 10:22 PM, Nathan Dunn <nat...@lb... <mailto:nat...@lb...>> wrote:
> Abhijit,
> 
> There are quite a few options.  
> 
> What is the purpose of the screen shots?  
> 
> Nathan
> 
> > On May 9, 2018, at 9:50 AM, Abhijit Sanyal <abh...@gm... <mailto:abh...@gm...>> wrote:
> > 
> > Hello,
> > 
> > I was wondering whether there was some script/module that one could run, on the command line, to capture screenshots in an automated fashion from Apollo. Using screen capture is too cumbersome since I have a lot of image captures to do.
> > 
> > Thanks
> > Abhijit
> > 
> > 
> > 
> > This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/ <http://genomearchitect.org/>
> > If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to sy...@li... <mailto:sy...@li...> | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank. 
> > 
> 
> 
> 
> 
> 
> This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/ <http://genomearchitect.org/>
> If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to sy...@li... <mailto:sy...@li...> | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank. 
> 
> 
> 
> 
> 
> 
> This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
> If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to sy...@li... | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank. 
> 

Re: [Gmod-ajax] Plugins not working with JBrowse-1.14.1-dev

[Vaneet L. <van...@uc...>]

Thanks Colin.  The latest release of the multibigwig repo fixed that bug.

I'm still having problems with the ComboTrackSelector plugin though, it loads fine but it draws the button for Faceted Track Selector over top of the Hierarchical track selector (screenshot attached of my example).

This is what the browser console printed when I accessed a genome using ComboTrackSelector:

Loaded ComboTrackSelector plugin
/JBrowse-1.14.1-dev/dist/0.bundle.js:41819 plugin HideTracksButton constructor
/JBrowse-1.14.1-dev/dist/0.bundle.js:41928 FeatureSequence plugin initialized.
/JBrowse-1.14.1-dev/dist/0.bundle.js:647 In JBrowse configuration, datasets specified, but dataset_id not set.  Dataset selector will not be shown.
(anonymous) @ /JBrowse-1.14.1-dev/dist/0.bundle.js:647
www.google-analytics.com/analytics.js Failed to load resource: net::ERR_BLOCKED_BY_CLIENT
circleIcon.png Failed to load resource: the server responded with a status of 404 (Not Found)

I believe the warning in yellow is okay, I don't want a dataset selector for this data directory, it's a test space for me, mainly testing this plugin.

Please let me know if there's anything I can fix to make the plugin work.

Vaneet

Vaneet Lotay
Xenbase Bioinformatician
716 ICT Building - University of Calgary
2500 University Drive NW
Calgary AB T2N 1N4
CANADA

From: Colin [mailto:col...@gm...]
Sent: Friday, May 04, 2018 6:46 PM
To: Robert Buels <rb...@gm...>
Cc: gmo...@li...
Subject: Re: [Gmod-ajax] Plugins not working with JBrowse-1.14.1-dev

With multibigwig at least, there was a bugfix added to support 1.14.1, should be able to pull this from multibigwig's GitHub repo and rerun setup

-Colin

On Fri, May 4, 2018, 8:14 PM Robert Buels <rb...@gm...<mailto:rb...@gm...>> wrote:
Are any errors shown in the browser's developer console?
On Fri, May 4, 2018 at 1:22 PM Nathan Dunn <nat...@lb...<mailto:nat...@lb...>> wrote:

You may want to open GitHub issues for the original plugins, as well.

GH pointers from here: https://gmod.github.io/jbrowse-registry/

Nathan


On May 4, 2018, at 1:14 PM, Vaneet Lotay <van...@uc...<mailto:van...@uc...>> wrote:

Hello,

I currently have JBrowse-1.13.1-dev installed, was looking to upgrade to version JBrowse-1.14-1-dev.  When I was testing the new version I noticed 2 of my additional plugins not working:

ComboTrackSelector
MultiBigWig

For the ComboTrackSelector plugin it still allows me to select the Faceted Track Selector, but it seems to place it right over the tracklist pane, that is it blocks the tracks on the Hierarchical track selector.  Whereas when the plugin is working properly it moves the tracks in the tracklist down to allow space for the click in button for the Faceted track selector.

For the MultiBigWig plugin I can see the track I produced via the MultiBigWig plugin but nothing is graphed on the track, no plot is drawn, I just see the track label.

This was all after I ran the setup.sh script and the 'npm run build' command by the way.

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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Re: [Gmod-ajax] Plugins not working with JBrowse-1.14.1-dev

[Colin <col...@gm...>]

With multibigwig at least, there was a bugfix added to support 1.14.1,
should be able to pull this from multibigwig's GitHub repo and rerun setup

-Colin

On Fri, May 4, 2018, 8:14 PM Robert Buels <rb...@gm...> wrote:

> Are any errors shown in the browser’s developer console?
> On Fri, May 4, 2018 at 1:22 PM Nathan Dunn <nat...@lb...> wrote:
>
>>
>> You may want to open GitHub issues for the original plugins, as well.
>>
>> GH pointers from here: https://gmod.github.io/jbrowse-registry/
>>
>> Nathan
>>
>>
>> On May 4, 2018, at 1:14 PM, Vaneet Lotay <van...@uc...>
>> wrote:
>>
>> Hello,
>>
>> I currently have JBrowse-1.13.1-dev installed, was looking to upgrade to
>> version JBrowse-1.14-1-dev.  When I was testing the new version I noticed 2
>> of my additional plugins not working:
>>
>> ComboTrackSelector
>> MultiBigWig
>>
>> For the ComboTrackSelector plugin it still allows me to select the
>> Faceted Track Selector, but it seems to place it right over the tracklist
>> pane, that is it blocks the tracks on the Hierarchical track selector.
>> Whereas when the plugin is working properly it moves the tracks in the
>> tracklist down to allow space for the click in button for the Faceted track
>> selector.
>>
>> For the MultiBigWig plugin I can see the track I produced via the
>> MultiBigWig plugin but nothing is graphed on the track, no plot is drawn, I
>> just see the track label.
>>
>> This was all after I ran the setup.sh script and the ‘npm run build’
>> command by the way.
>>
>> Thanks,
>>
>> Vaneet
>>
>>
>>
>> *Vaneet Lotay*
>>
>> *Xenbase Bioinformatician*
>>
>> *716 ICT Building - University of Calgary*
>>
>> *2500 University Drive NW*
>>
>> *Calgary AB T2N 1N4*
>>
>> *CANADA*
>>
>>
>> ------------------------------------------------------------------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org <http://slashdot.org/>!
>> http://sdm.link/slashdot_______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

Re: [Gmod-ajax] Plugins not working with JBrowse-1.14.1-dev

[Robert B. <rb...@gm...>]

Are any errors shown in the browser’s developer console?
On Fri, May 4, 2018 at 1:22 PM Nathan Dunn <nat...@lb...> wrote:

>
> You may want to open GitHub issues for the original plugins, as well.
>
> GH pointers from here: https://gmod.github.io/jbrowse-registry/
>
> Nathan
>
>
> On May 4, 2018, at 1:14 PM, Vaneet Lotay <van...@uc...> wrote:
>
> Hello,
>
> I currently have JBrowse-1.13.1-dev installed, was looking to upgrade to
> version JBrowse-1.14-1-dev.  When I was testing the new version I noticed 2
> of my additional plugins not working:
>
> ComboTrackSelector
> MultiBigWig
>
> For the ComboTrackSelector plugin it still allows me to select the Faceted
> Track Selector, but it seems to place it right over the tracklist pane,
> that is it blocks the tracks on the Hierarchical track selector.  Whereas
> when the plugin is working properly it moves the tracks in the tracklist
> down to allow space for the click in button for the Faceted track selector.
>
> For the MultiBigWig plugin I can see the track I produced via the
> MultiBigWig plugin but nothing is graphed on the track, no plot is drawn, I
> just see the track label.
>
> This was all after I ran the setup.sh script and the ‘npm run build’
> command by the way.
>
> Thanks,
>
> Vaneet
>
>
>
> *Vaneet Lotay*
>
> *Xenbase Bioinformatician*
>
> *716 ICT Building - University of Calgary*
>
> *2500 University Drive NW*
>
> *Calgary AB T2N 1N4*
>
> *CANADA*
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org <http://slashdot.org/>!
> http://sdm.link/slashdot_______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

Re: [Gmod-ajax] Plugins not working with JBrowse-1.14.1-dev

[Nathan D. <nat...@lb...>]

You may want to open GitHub issues for the original plugins, as well.

GH pointers from here: https://gmod.github.io/jbrowse-registry/ <https://gmod.github.io/jbrowse-registry/>

Nathan


> On May 4, 2018, at 1:14 PM, Vaneet Lotay <van...@uc...> wrote:
> 
> Hello,
>  
> I currently have JBrowse-1.13.1-dev installed, was looking to upgrade to version JBrowse-1.14-1-dev.  When I was testing the new version I noticed 2 of my additional plugins not working:
>  
> ComboTrackSelector
> MultiBigWig
>  
> For the ComboTrackSelector plugin it still allows me to select the Faceted Track Selector, but it seems to place it right over the tracklist pane, that is it blocks the tracks on the Hierarchical track selector.  Whereas when the plugin is working properly it moves the tracks in the tracklist down to allow space for the click in button for the Faceted track selector.
>  
> For the MultiBigWig plugin I can see the track I produced via the MultiBigWig plugin but nothing is graphed on the track, no plot is drawn, I just see the track label.
>  
> This was all after I ran the setup.sh script and the ‘npm run build’ command by the way.
>  
> Thanks,
>  
> Vaneet
>  
>  
> Vaneet Lotay
> 
> Xenbase Bioinformatician
> 
> 716 ICT Building - University of Calgary
> 
> 2500 University Drive NW
> 
> Calgary AB T2N 1N4
> 
> CANADA
> 
>  
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org <http://slashdot.org/>! http://sdm.link/slashdot_______________________________________________ <http://sdm.link/slashdot_______________________________________________>
> Gmod-ajax mailing list
> Gmo...@li... <mailto:Gmo...@li...>
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax <https://lists.sourceforge.net/lists/listinfo/gmod-ajax>

[Gmod-ajax] Plugins not working with JBrowse-1.14.1-dev

[Vaneet L. <van...@uc...>]

Hello,

I currently have JBrowse-1.13.1-dev installed, was looking to upgrade to version JBrowse-1.14-1-dev.  When I was testing the new version I noticed 2 of my additional plugins not working:

ComboTrackSelector
MultiBigWig

For the ComboTrackSelector plugin it still allows me to select the Faceted Track Selector, but it seems to place it right over the tracklist pane, that is it blocks the tracks on the Hierarchical track selector.  Whereas when the plugin is working properly it moves the tracks in the tracklist down to allow space for the click in button for the Faceted track selector.

For the MultiBigWig plugin I can see the track I produced via the MultiBigWig plugin but nothing is graphed on the track, no plot is drawn, I just see the track label.

This was all after I ran the setup.sh script and the 'npm run build' command by the way.

Thanks,

Vaneet



Vaneet Lotay

Xenbase Bioinformatician

716 ICT Building - University of Calgary

2500 University Drive NW

Calgary AB T2N 1N4

CANADA

Re: [Gmod-ajax] jbrowse looking for root.json despite having run generate-names.pl

[Seth M. <mu...@uw...>]

Well it's something to do with my out option setup.  I reloaded it from the
jbrowse root directory and everything worked like a charm.

Thanks for pointing out the website issue as well, for some reason the
router isn't redirecting traffic from outisde the university to the correct
machine.  I'll need to fix that as well.

Seth Munholland, Ph.D. Candidate
VP, Finance & Extracurricular Affairs, DBGSA
Department of Biological Sciences
Rm. 304 Biology Building
University of Windsor
401 Sunset Ave. N9B 3P4
T: (519) 253-3000 Ext: 4755

On Fri, May 4, 2018 at 3:06 PM, Scott Cain <sc...@sc...> wrote:

> Hi Seth,
>
> Unfortunately, it looks like the url to your jbrowse isn't working--I'm
> guessing it's sitting behind a firewall.
>
> Generally you don't put stuff in the data directory yourself, rather the
> prep scripts (prepare_refseqs and flatfile_to_json) handle putting files in
> there for you, so that everything is formatted properly and in the right
> place.  While you're figuring out the basics, I'd suggest you not use the
> "out" options for the command line scripts, so that the processed data will
> be in the default locations.  Additionally, you usually supply a "--type"
> argument to the flatfile script indicating what things should be put in the
> track.  Given the name of the file, I'm guessing you'd want "gene" as the
> value.  The flatfile script knows to get all of the children features of
> genes and group them together appropriately.
>
> Good luck and let us know if you need any more help,
> Scott
>
> PS: I'm glad to see you decided to switch to JBrowse; I almost always
> suggest that when answering GBrowse help requests :-)
>
> On Fri, May 4, 2018 at 2:30 PM, Seth Munholland <mu...@uw...>
> wrote:
>
>> Hi Everyone,
>>
>> New to JBrowse and trying to get my data to show.  I had it formatted for
>> GBrowse so I know can work.  I made a /data directory in my jbrowse
>> directory, put my fasta and genemodels gff in there to start with and used
>> the following commands in jbrowse/data:
>>
>> prepare-refseqs.pl --fasta OAC-Rex_Pseudochromosomes_V3.3.fa -o OAC-Rex
>>
>> flatfile-to-json.pl --gff OAC-Rex_Pseudochromosomes_V3.3_genemodels.gff
>> --trackType CanvasFeatures --trackLabel mygff --out OAC-Rex
>>
>> generate-names.pl -v --out OAC-Rex
>>
>> When I go to my jbrowse (www.bioinfo.uwindsor.ca/jbrowse) and select
>> OAC-Rex I get the grid and drop down list of the first 30 scaffolds I have,
>> but no tracks are loading, not even the sequence data.  When I look at my
>> console I see 2 entries:
>>
>> 1) ML Parsing Error: not well-formed Location:
>> http://www.bioinfo.uwindsor.ca/jbrowse/jbrowse.conf Line Number 1,
>> Column 2: jbrowse.conf:1:2
>> <http://www.bioinfo.uwindsor.ca/jbrowse/jbrowse.conf>
>> 2) Object { message: "Unable to load data/OAC-Rex/names/root.json
>> status: 404"
>>
>> The first makes no sense to me as I don't see columns on line 1 and the
>> title is still being applied to the tab in my browser.
>> The second makes no sense because (if I understood jbrowse's docs
>> properly) root.json should only be looked for if generate-names.pl has
>> not been run.  I even have the snippet at the top of
>> data/OAC-Rex/trackList.json from it:
>>
>> ...
>>    "names" : {
>>       "type" : "Hash",
>>       "url" : "names/"
>>    },
>> ...
>>
>> Any ideas?
>>
>> Seth Munholland, Ph.D. Candidate
>> VP, Finance & Extracurricular Affairs, DBGSA
>> Department of Biological Sciences
>> Rm. 304 Biology Building
>> University of Windsor
>> 401 Sunset Ave. N9B 3P4
>> <https://maps.google.com/?q=401+Sunset+Ave.+N9B+3P4&entry=gmail&source=g>
>> T: (519) 253-3000 Ext: 4755
>>
>> ------------------------------------------------------------
>> ------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> _______________________________________________
>> 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
>

Re: [Gmod-ajax] jbrowse looking for root.json despite having run generate-names.pl

[Scott C. <sc...@sc...>]

Hi Seth,

Unfortunately, it looks like the url to your jbrowse isn't working--I'm
guessing it's sitting behind a firewall.

Generally you don't put stuff in the data directory yourself, rather the
prep scripts (prepare_refseqs and flatfile_to_json) handle putting files in
there for you, so that everything is formatted properly and in the right
place.  While you're figuring out the basics, I'd suggest you not use the
"out" options for the command line scripts, so that the processed data will
be in the default locations.  Additionally, you usually supply a "--type"
argument to the flatfile script indicating what things should be put in the
track.  Given the name of the file, I'm guessing you'd want "gene" as the
value.  The flatfile script knows to get all of the children features of
genes and group them together appropriately.

Good luck and let us know if you need any more help,
Scott

PS: I'm glad to see you decided to switch to JBrowse; I almost always
suggest that when answering GBrowse help requests :-)

On Fri, May 4, 2018 at 2:30 PM, Seth Munholland <mu...@uw...> wrote:

> Hi Everyone,
>
> New to JBrowse and trying to get my data to show.  I had it formatted for
> GBrowse so I know can work.  I made a /data directory in my jbrowse
> directory, put my fasta and genemodels gff in there to start with and used
> the following commands in jbrowse/data:
>
> prepare-refseqs.pl --fasta OAC-Rex_Pseudochromosomes_V3.3.fa -o OAC-Rex
>
> flatfile-to-json.pl --gff OAC-Rex_Pseudochromosomes_V3.3_genemodels.gff
> --trackType CanvasFeatures --trackLabel mygff --out OAC-Rex
>
> generate-names.pl -v --out OAC-Rex
>
> When I go to my jbrowse (www.bioinfo.uwindsor.ca/jbrowse) and select
> OAC-Rex I get the grid and drop down list of the first 30 scaffolds I have,
> but no tracks are loading, not even the sequence data.  When I look at my
> console I see 2 entries:
>
> 1) ML Parsing Error: not well-formed Location:
> http://www.bioinfo.uwindsor.ca/jbrowse/jbrowse.conf Line Number 1, Column
> 2: jbrowse.conf:1:2 <http://www.bioinfo.uwindsor.ca/jbrowse/jbrowse.conf>
> 2) Object { message: "Unable to load data/OAC-Rex/names/root.json status:
> 404"
>
> The first makes no sense to me as I don't see columns on line 1 and the
> title is still being applied to the tab in my browser.
> The second makes no sense because (if I understood jbrowse's docs
> properly) root.json should only be looked for if generate-names.pl has
> not been run.  I even have the snippet at the top of
> data/OAC-Rex/trackList.json from it:
>
> ...
>    "names" : {
>       "type" : "Hash",
>       "url" : "names/"
>    },
> ...
>
> Any ideas?
>
> Seth Munholland, Ph.D. Candidate
> VP, Finance & Extracurricular Affairs, DBGSA
> Department of Biological Sciences
> Rm. 304 Biology Building
> University of Windsor
> 401 Sunset Ave. N9B 3P4
> T: (519) 253-3000 Ext: 4755
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> 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

[Gmod-ajax] jbrowse looking for root.json despite having run generate-names.pl

[Seth M. <mu...@uw...>]

Hi Everyone,

New to JBrowse and trying to get my data to show.  I had it formatted for
GBrowse so I know can work.  I made a /data directory in my jbrowse
directory, put my fasta and genemodels gff in there to start with and used
the following commands in jbrowse/data:

prepare-refseqs.pl --fasta OAC-Rex_Pseudochromosomes_V3.3.fa -o OAC-Rex

flatfile-to-json.pl --gff OAC-Rex_Pseudochromosomes_V3.3_genemodels.gff
--trackType CanvasFeatures --trackLabel mygff --out OAC-Rex

generate-names.pl -v --out OAC-Rex

When I go to my jbrowse (www.bioinfo.uwindsor.ca/jbrowse) and select
OAC-Rex I get the grid and drop down list of the first 30 scaffolds I have,
but no tracks are loading, not even the sequence data.  When I look at my
console I see 2 entries:

1) ML Parsing Error: not well-formed Location:
http://www.bioinfo.uwindsor.ca/jbrowse/jbrowse.conf Line Number 1, Column 2:
jbrowse.conf:1:2 <http://www.bioinfo.uwindsor.ca/jbrowse/jbrowse.conf>
2) Object { message: "Unable to load data/OAC-Rex/names/root.json status:
404"

The first makes no sense to me as I don't see columns on line 1 and the
title is still being applied to the tab in my browser.
The second makes no sense because (if I understood jbrowse's docs properly)
root.json should only be looked for if generate-names.pl has not been run.
I even have the snippet at the top of data/OAC-Rex/trackList.json from it:

...
   "names" : {
      "type" : "Hash",
      "url" : "names/"
   },
...

Any ideas?

Seth Munholland, Ph.D. Candidate
VP, Finance & Extracurricular Affairs, DBGSA
Department of Biological Sciences
Rm. 304 Biology Building
University of Windsor
401 Sunset Ave. N9B 3P4
T: (519) 253-3000 Ext: 4755

Re: [Gmod-ajax] [apollo] GMOD in the Cloud with docker

[Nathan D. <nat...@lb...>]

I think there are some great starting points here, from Eric, Bjorn and Antony, though they are also out of date: 

https://github.com/galaxy-genome-annotation/ <https://github.com/galaxy-genome-annotation/>


https://github.com/galaxy-genome-annotation/dockerized-gmod-deployment <https://github.com/galaxy-genome-annotation/dockerized-gmod-deployment>
https://github.com/galaxy-genome-annotation/docker-galaxy-genome-annotation <https://github.com/galaxy-genome-annotation/docker-galaxy-genome-annotation>


Apollo has its own version (for a quick start): https://github.com/GMOD/docker-apollo <https://github.com/GMOD/docker-apollo>, but I have a feeling you’ll want wants above. 

I’m sure that there are a few other galaxy projects that do a full-scale integration. 

Nathan



> On May 4, 2018, at 7:35 AM, Scott Cain <sc...@sc...> wrote:
> 
> Hi All,
> 
> I'm thinking about creating a new GMOD in the Cloud to replace the now very old one.  Since technology has advanced quite a bit since I last did this, I'm thinking I might be able to use docker to do it all.  This instance would contain Chado, Tripal, JBrowse and Apollo.  Are there "canonical" docker images for all of these?  I assume I'll probably want to modify them to work together in a nice way, but having a good starting point would be nice.
> 
> Also, do you have any suggestions for what else should be included?  I figured I would put in some yeast sample data, but having some sample data that could be edited by Apollo and be integrated into Tripal would be really nice.
> 
> Thanks,
> Scott
> 
> 
> -- 
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/ <http://gmod.org/>)                     216-392-3087
> Ontario Institute for Cancer Research
> 
> 
> 
> This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
> If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to sy...@li... | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank. 
> 

[Gmod-ajax] GMOD in the Cloud with docker

[Scott C. <sc...@sc...>]

Hi All,

I'm thinking about creating a new GMOD in the Cloud to replace the now very
old one.  Since technology has advanced quite a bit since I last did this,
I'm thinking I might be able to use docker to do it all.  This instance
would contain Chado, Tripal, JBrowse and Apollo.  Are there "canonical"
docker images for all of these?  I assume I'll probably want to modify them
to work together in a nice way, but having a good starting point would be
nice.

Also, do you have any suggestions for what else should be included?  I
figured I would put in some yeast sample data, but having some sample data
that could be edited by Apollo and be integrated into Tripal would be
really nice.

Thanks,
Scott


-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

[Gmod-ajax] JBrowse 1.14.1 released!

[Robert B. <rb...@gm...>]

JBrowse 1.14.1 has been released!
Files for download

   - JBrowse-1.14.1.zip
   <https://github.com/GMOD/jbrowse/releases/download/1.14.1-release/JBrowse-1.14.1.zip>
–
   2.8M
   file SHA1 f41c89826db00afc4b78a37a255aa6b43c3df986
   - JBrowse-1.14.1-dev.zip
   <https://github.com/GMOD/jbrowse/releases/download/1.14.1-release/JBrowse-1.14.1-dev.zip>
–
   7.5M
   file SHA1 5a2e119c08790eb81dc6ae2ac8cf7483093ac9e5

Minor improvements

   -

   JBrowse now supports .idx indexes for VCFs that are generated by igvtools or
   GATK. Currently
   only VCF files can be used with this index type, but this could be
   expanded to other file types
   if users are interested. Thanks to @thon-deboer
   <https://github.com/thon-deboer> for suggesting this! (issue #1019
   <https://github.com/gmod/jbrowse/issues/1019>, @rbuels
   <https://github.com/rbuels>)
   -

   The dropdown dataset selector in “classic menu” mode is now a type-ahead
   combo box, enabling
   fast searching through large numbers of datasets. Thanks to @keiranmraine
   <https://github.com/keiranmraine> for the suggestion!
   (issue #752 <https://github.com/gmod/jbrowse/issues/752>, @rbuels
   <https://github.com/rbuels>)
   -

   There is now a new event named /jbrowse/v1/n/tracks/redrawFinished that
   fires after the
   view is refreshed, when all of the visible tracks are finished drawing
   (or have errored).
   Thanks to @scottcain <https://github.com/scottcain> for suggesting this.
   (issue #1027 <https://github.com/gmod/jbrowse/issues/1027>, @rbuels
   <https://github.com/rbuels>)
   -

   Improve the calculation of feature density for GFF3Tabix and add new one
   for GFF3 in-memory.
   Thanks to @hkmoon <https://github.com/hkmoon> for the suggestion! (issue
   #1039 <https://github.com/gmod/jbrowse/issues/1039>, issue #913
   <https://github.com/gmod/jbrowse/issues/913>, @cmdcolin
   <https://github.com/cmdcolin>)
   -

   Re-enabled JBrowse Desktop builds based on automatically building on
   Travis-CI
   (issue #1028 <https://github.com/gmod/jbrowse/issues/1028>, @cmdcolin
   <https://github.com/cmdcolin>)

Bug fixes

   -

   Fixed several bugs related to the file-opening dialog’s handling of
   indexed file types
   (bam+bai, gz+tbi, etc). Thanks to @sletort <https://github.com/sletort> for
   submitting the bug report! (issue #1033
   <https://github.com/gmod/jbrowse/issues/1033>, @rbuels
   <https://github.com/rbuels>)
   -

   The Perl formatting tools now properly read include-ed configuration
   files. Thanks to @carrere <https://github.com/carrere>
   for pointing out this bug. (issue #551
   <https://github.com/gmod/jbrowse/issues/551>, @rbuels
   <https://github.com/rbuels>)
   -

   Fixed a bug in which the faceted track selector was nonfunctional in
   Internet Explorer 11.
   (issue #1036 <https://github.com/gmod/jbrowse/issues/1036>, @rbuels
   <https://github.com/rbuels>)

Re: [Gmod-ajax] Fw: ./setup.sh issues

[Robert B. <rb...@gm...>]

Node isn’t required for the regular release, just for -dev releases (which
include all the source code, and which only people that need to install
third-party plugins will need).

Scott, are you sure about the SHA sums of the downloads being wrong?  I
just checked, they look right to me.  Console session attached for proof.
:-)



On Fri, Apr 27, 2018 at 1:54 PM Jonathan McMillan <jon...@sl...>
wrote:

> Downloaded Nodejs and retried the download, seems to be a success! Thanks
> so much for the help today!
>
>
> Thanks,
>
> Jonathan McMillan
> ------------------------------
> *From:* Jonathan McMillan
> *Sent:* Friday, April 27, 2018 3:37:53 PM
> *To:* Scott Cain; Robert Buels; Eric Yao
>
> *Cc:* gmo...@li...
> *Subject:* Re: [Gmod-ajax] Fw: ./setup.sh issues
>
> So I had been using curl to grab the zip file from github, trying to unzip
> files grabbed from curl would not unzip. Tried wget and worked first time!
>
>
> Tried ./setup.sh again, which failed. This is the .log file, do I need to
> download node.js onto my machine in order to download JBrowse?
>
> <https://drive.google.com/open?id=1nksTM4y3qCa2_k3IsGPs4EuWMK860DT3>
> https://drive.google.com/file/d/1nksTM4y3qCa2_k3IsGPs4EuWMK860DT3/view?usp=sharing
>
> <https://drive.google.com/file/d/1nksTM4y3qCa2_k3IsGPs4EuWMK860DT3/view?usp=sharing>
> setup.log
> <https://drive.google.com/file/d/1nksTM4y3qCa2_k3IsGPs4EuWMK860DT3/view?usp=sharing>
> drive.google.com
> Thanks,
>
> Jonathan McMillan
>
> ------------------------------
> *From:* Scott Cain <sc...@sc...>
> *Sent:* Friday, April 27, 2018 2:42:15 PM
> *To:* Jonathan McMillan; Robert Buels; Eric Yao
> *Cc:* gmo...@li...
> *Subject:* Re: [Gmod-ajax] Fw: ./setup.sh issues
>
> And I just noticed there isn't a tar.gz file (there always used to be!)
> Sorry about that; another thing I'd suggest is using a different browser or
> using something like curl or wget to retrieve it.
>
>
> On Fri, Apr 27, 2018 at 3:40 PM, Scott Cain <sc...@sc...> wrote:
>
> Hi Jonathan,
>
> Perhaps the download got truncated? I just downloaded 1.14.0.zip and it
> unzipped fine, ALTHOUGH (and this is directed at Rob and Eric), when I did
> the md5sum of the downloaded zip file it does not match the md5 sum
> reported on the website, which is a bit of a problem.  Could you guys check
> that out?
>
> Back to Jonathan: if downloading the zip file doesn't work, perhaps you
> could use the tar.gz file instead?
>
> Scott
>
>
> On Fri, Apr 27, 2018 at 1:45 PM, Jonathan McMillan <
> jon...@sl...> wrote:
>
> Hey again,
>
>
> So I have the zip file downloaded from the github repo. But now when I try
> to unzip the file in my webserver there seems to be an error.
>
> This is the output from my machine.
>
> [ec2-user@###### jbrowse]$ unzip JBrowse-1.14.0.zip
> Archive:  JBrowse-1.14.0.zip
>   End-of-central-directory signature not found.  Either this file is not
>   a zipfile, or it constitutes one disk of a multi-part archive.  In the
>   latter case the central directory and zipfile comment will be found on
>   the last disk(s) of this archive.
> unzip:  cannot find zipfile directory in one of JBrowse-1.14.0.zip or
>         JBrowse-1.14.0.zip.zip, and cannot find JBrowse-1.14.0.zip.ZIP,
> period.
>
> [ec2-user@###### jbrowse]$ file JBrowse-1.14.0.zip
> JBrowse-1.14.0.zip: HTML document, ASCII text, with very long lines, with
> no line terminators
>
> Thanks for all the help,
>
> Jonathan McMillan
> ------------------------------
> *From:* Jonathan McMillan
> *Sent:* Friday, April 27, 2018 11:52:00 AM
> *To:* Scott Cain
>
> *Cc:* gmo...@li...
> *Subject:* Re: [Gmod-ajax] Fw: ./setup.sh issues
>
>
> No specific reason, was just follwing the JBrowse quick start guide
> http://jbrowse.org/code/JBrowse-1.14.0/docs/tutorial/index.html
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__jbrowse.org_code_JBrowse-2D1.14.0_docs_tutorial_index.html&d=DwMFaQ&c=Pk_HpaIpE_jAoEC9PLIWoQ&r=tHmIv0YuoIPeACKiRmuf9tkl4ot_m-78ai1jalYUtZo&m=ZRWhaUFyclCWuHHrcb6XuPtdWtzGFkuDsVScf75KZg8&s=kT5q-_XUgRtbCgd4oslywdvhX5JA1PGuChAtmnPUNGU&e=>
>
> I will try it with 1.14
>
>
> Thanks,
>
> Jonathan McMillan
> ------------------------------
> *From:* Scott Cain <sc...@sc...>
> *Sent:* Friday, April 27, 2018 11:33:21 AM
> *To:* Jonathan McMillan
> *Cc:* gmo...@li...
> *Subject:* Re: [Gmod-ajax] Fw: ./setup.sh issues
>
> Hi Jonathan,
>
> Much better--thanks!
>
> It looks like you are trying to install a very old version of JBrowse, 1.8
> (we are on 1.14) and it is failing trying to install SAMtools.  Is there a
> reason you want to use such an old version?
>
> Scott
>
>
> On Fri, Apr 27, 2018 at 12:08 PM, Jonathan McMillan <
> jon...@sl...> wrote:
>
>
>
>
> ------------------------------
> *From:* Jon McMillan <jon...@ao...>
> *Sent:* Friday, April 27, 2018 11:06 AM
> *To:* Jonathan McMillan
> *Subject:* Re: [Gmod-ajax] ./setup.sh issues
>
> Apologies for the sharepoint issues. Hope this works better.
>
> Thanks,
> Jonathan McMillan
>
>
> -----Original Message-----
> From: Jonathan McMillan <jon...@sl...>
> To: Jon McMillan <jon...@ao...>
> Sent: Fri, Apr 27, 2018 10:44 am
> Subject: Fwd: [Gmod-ajax] ./setup.sh issues
>
>
>
> Get Outlook for Android
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__aka.ms_ghei36&d=DwMCaQ&c=Pk_HpaIpE_jAoEC9PLIWoQ&r=tHmIv0YuoIPeACKiRmuf9tkl4ot_m-78ai1jalYUtZo&m=BwD5ccOnH5jug6GXgCrIOTGVCnotmb9fPWUt_I8DQTA&s=PBf-VBKWIBSAIhwPw9nWL0l0KEsg6_Yl7cWoVexoLzY&e=>
>
> ------------------------------
> *From:* Robert Buels <rb...@gm...>
> *Sent:* Friday, April 27, 2018 10:27:54 AM
> *To:* Jonathan McMillan
> *Cc:* gmo...@li...
> *Subject:* Re: [Gmod-ajax] ./setup.sh issues
>
> Hi Jonathan,
>
> Could you simply attach the files to the email or paste them into the
> body? Many of us do not have Microsoft accounts to log in to onedrive.
>
>
>
>
> On Fri, Apr 27, 2018 at 8:02 AM Jonathan McMillan <
> jon...@sl...> wrote:
>
> Jonathan McMillan has shared OneDrive for Business files with you. To view
> them, click the links below.
>
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__sluedu-2Dmy.sharepoint.com_personal_jonathan-5Fmcmillan-5Fslu-5Fedu_Documents_Attachments_setup.log&d=DwMFaQ&c=Pk_HpaIpE_jAoEC9PLIWoQ&r=tHmIv0YuoIPeACKiRmuf9tkl4ot_m-78ai1jalYUtZo&m=WA7bUWjYcZJRlRdK9SqjMelunBgqpV2T1ivw6Wrv-dQ&s=sg6-NNJPT6yp3HZwoHznbVzJNRXz_9jTzw6q6qXTI54&e=>
> setup.log
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__sluedu-2Dmy.sharepoint.com_personal_jonathan-5Fmcmillan-5Fslu-5Fedu_Documents_Attachments_setup.log&d=DwMFaQ&c=Pk_HpaIpE_jAoEC9PLIWoQ&r=tHmIv0YuoIPeACKiRmuf9tkl4ot_m-78ai1jalYUtZo&m=WA7bUWjYcZJRlRdK9SqjMelunBgqpV2T1ivw6Wrv-dQ&s=sg6-NNJPT6yp3HZwoHznbVzJNRXz_9jTzw6q6qXTI54&e=>
>
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__sluedu-2Dmy.sharepoint.com_personal_jonathan-5Fmcmillan-5Fslu-5Fedu_Documents_Attachments_setup.log&d=DwMFaQ&c=Pk_HpaIpE_jAoEC9PLIWoQ&r=tHmIv0YuoIPeACKiRmuf9tkl4ot_m-78ai1jalYUtZo&m=WA7bUWjYcZJRlRdK9SqjMelunBgqpV2T1ivw6Wrv-dQ&s=sg6-NNJPT6yp3HZwoHznbVzJNRXz_9jTzw6q6qXTI54&e=>
>
>
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__sluedu-2Dmy.sharepoint.com_personal_jonathan-5Fmcmillan-5Fslu-5Fedu_Documents_Attachments_setup-5Foutput.txt&d=DwMFaQ&c=Pk_HpaIpE_jAoEC9PLIWoQ&r=tHmIv0YuoIPeACKiRmuf9tkl4ot_m-78ai1jalYUtZo&m=WA7bUWjYcZJRlRdK9SqjMelunBgqpV2T1ivw6Wrv-dQ&s=Jq0Y1NAg9UY9i-9CJVdXdqgp_cDUnKR75F3m8Me3pfg&e=>
> setup_output.txt
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__sluedu-2Dmy.sharepoint.com_personal_jonathan-5Fmcmillan-5Fslu-5Fedu_Documents_Attachments_setup-5Foutput.txt&d=DwMFaQ&c=Pk_HpaIpE_jAoEC9PLIWoQ&r=tHmIv0YuoIPeACKiRmuf9tkl4ot_m-78ai1jalYUtZo&m=WA7bUWjYcZJRlRdK9SqjMelunBgqpV2T1ivw6Wrv-dQ&s=Jq0Y1NAg9UY9i-9CJVdXdqgp_cDUnKR75F3m8Me3pfg&e=>
>
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__sluedu-2Dmy.sharepoint.com_personal_jonathan-5Fmcmillan-5Fslu-5Fedu_Documents_Attachments_setup-5Foutput.txt&d=DwMFaQ&c=Pk_HpaIpE_jAoEC9PLIWoQ&r=tHmIv0YuoIPeACKiRmuf9tkl4ot_m-78ai1jalYUtZo&m=WA7bUWjYcZJRlRdK9SqjMelunBgqpV2T1ivw6Wrv-dQ&s=Jq0Y1NAg9UY9i-9CJVdXdqgp_cDUnKR75F3m8Me3pfg&e=>
> Hi,
>
> I was having some issues with ./setup.sh
>
> Here is the setup.log file and the txt file is the output from running
> ./setup.sh . An help is greatly appreciated!
>
> Thanks,
> Joanthan McMillan
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__sdm.link_slashdot&d=DwMFaQ&c=Pk_HpaIpE_jAoEC9PLIWoQ&r=tHmIv0YuoIPeACKiRmuf9tkl4ot_m-78ai1jalYUtZo&m=WA7bUWjYcZJRlRdK9SqjMelunBgqpV2T1ivw6Wrv-dQ&s=JlMFpXK90-w3QuIk8KYb7xAQ2MVZDvKVeBVJmHARWaQ&e=>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.sourceforge.net_lists_listinfo_gmod-2Dajax&d=DwMFaQ&c=Pk_HpaIpE_jAoEC9PLIWoQ&r=tHmIv0YuoIPeACKiRmuf9tkl4ot_m-78ai1jalYUtZo&m=WA7bUWjYcZJRlRdK9SqjMelunBgqpV2T1ivw6Wrv-dQ&s=kl-JevJ4UBXXIFbdpTwyqnubj-LLrkOIfW7XkSzWRX0&e=>
>
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__sdm.link_slashdot&d=DwMFaQ&c=Pk_HpaIpE_jAoEC9PLIWoQ&r=tHmIv0YuoIPeACKiRmuf9tkl4ot_m-78ai1jalYUtZo&m=HRli8jHaIHMVdCKDPLv0IW0dfeJJPYQcvJs6mpNaEQc&s=djC5tmHwZGmEK5jMGrlEFkEebPbACLpVykK9I0LeUao&e=>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.sourceforge.net_lists_listinfo_gmod-2Dajax&d=DwMFaQ&c=Pk_HpaIpE_jAoEC9PLIWoQ&r=tHmIv0YuoIPeACKiRmuf9tkl4ot_m-78ai1jalYUtZo&m=HRli8jHaIHMVdCKDPLv0IW0dfeJJPYQcvJs6mpNaEQc&s=PdpbCK211WVSilNPsAoRfuZOjyXtmPG7cgw9-rAr4kI&e=>
>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain
> dot net
> GMOD Coordinator (http://gmod.org/
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__gmod.org_&d=DwMFaQ&c=Pk_HpaIpE_jAoEC9PLIWoQ&r=tHmIv0YuoIPeACKiRmuf9tkl4ot_m-78ai1jalYUtZo&m=HRli8jHaIHMVdCKDPLv0IW0dfeJJPYQcvJs6mpNaEQc&s=UwH0VICRAUVx4vFSkKOuWEujt05Z7kukb4F92OMpUzE&e=>)
>                    216-392-3087 <(216)%20392-3087>
> Ontario Institute for Cancer Research
>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain
> dot net
> GMOD Coordinator (http://gmod.org/
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__gmod.org_&d=DwMFaQ&c=Pk_HpaIpE_jAoEC9PLIWoQ&r=tHmIv0YuoIPeACKiRmuf9tkl4ot_m-78ai1jalYUtZo&m=ZRWhaUFyclCWuHHrcb6XuPtdWtzGFkuDsVScf75KZg8&s=TiSJVixFjcZ_D1J6JbTy5PhdI7mN3DAVyBNE4kxX1Hg&e=>)
>                    216-392-3087 <(216)%20392-3087>
> Ontario Institute for Cancer Research
>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain
> dot net
> GMOD Coordinator (http://gmod.org/
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__gmod.org_&d=DwMFaQ&c=Pk_HpaIpE_jAoEC9PLIWoQ&r=tHmIv0YuoIPeACKiRmuf9tkl4ot_m-78ai1jalYUtZo&m=ZRWhaUFyclCWuHHrcb6XuPtdWtzGFkuDsVScf75KZg8&s=TiSJVixFjcZ_D1J6JbTy5PhdI7mN3DAVyBNE4kxX1Hg&e=>)
>                    216-392-3087 <(216)%20392-3087>
> Ontario Institute for Cancer Research
>

Re: [Gmod-ajax] Fw: ./setup.sh issues

[Jonathan M. <jon...@sl...>]

So I had been using curl to grab the zip file from github, trying to unzip files grabbed from curl would not unzip. Tried wget and worked first time!


Tried ./setup.sh again, which failed. This is the .log file, do I need to download node.js onto my machine in order to download JBrowse?

<https://drive.google.com/open?id=1nksTM4y3qCa2_k3IsGPs4EuWMK860DT3>https://drive.google.com/file/d/1nksTM4y3qCa2_k3IsGPs4EuWMK860DT3/view?usp=sharing

[https://lh6.googleusercontent.com/2ezWPRTpAPpp_x5RJrg0RwsidCtLosVJVrrQeyrfdC9kNXXRglJ_jSHyeOs=w1200-h630-p]<https://drive.google.com/file/d/1nksTM4y3qCa2_k3IsGPs4EuWMK860DT3/view?usp=sharing>

setup.log<https://drive.google.com/file/d/1nksTM4y3qCa2_k3IsGPs4EuWMK860DT3/view?usp=sharing>
drive.google.com

Thanks,

Jonathan McMillan

________________________________
From: Scott Cain <sc...@sc...>
Sent: Friday, April 27, 2018 2:42:15 PM
To: Jonathan McMillan; Robert Buels; Eric Yao
Cc: gmo...@li...
Subject: Re: [Gmod-ajax] Fw: ./setup.sh issues

And I just noticed there isn't a tar.gz file (there always used to be!)  Sorry about that; another thing I'd suggest is using a different browser or using something like curl or wget to retrieve it.


On Fri, Apr 27, 2018 at 3:40 PM, Scott Cain <sc...@sc...<mailto:sc...@sc...>> wrote:
Hi Jonathan,

Perhaps the download got truncated? I just downloaded 1.14.0.zip and it unzipped fine, ALTHOUGH (and this is directed at Rob and Eric), when I did the md5sum of the downloaded zip file it does not match the md5 sum reported on the website, which is a bit of a problem.  Could you guys check that out?

Back to Jonathan: if downloading the zip file doesn't work, perhaps you could use the tar.gz file instead?

Scott


On Fri, Apr 27, 2018 at 1:45 PM, Jonathan McMillan <jon...@sl...<mailto:jon...@sl...>> wrote:

Hey again,


So I have the zip file downloaded from the github repo. But now when I try to unzip the file in my webserver there seems to be an error.

This is the output from my machine.

[ec2-user@###### jbrowse]$ unzip JBrowse-1.14.0.zip
Archive:  JBrowse-1.14.0.zip
  End-of-central-directory signature not found.  Either this file is not
  a zipfile, or it constitutes one disk of a multi-part archive.  In the
  latter case the central directory and zipfile comment will be found on
  the last disk(s) of this archive.
unzip:  cannot find zipfile directory in one of JBrowse-1.14.0.zip or
        JBrowse-1.14.0.zip.zip, and cannot find JBrowse-1.14.0.zip.ZIP, period.

[ec2-user@###### jbrowse]$ file JBrowse-1.14.0.zip
JBrowse-1.14.0.zip: HTML document, ASCII text, with very long lines, with no line terminators

Thanks for all the help,

Jonathan McMillan

________________________________
From: Jonathan McMillan
Sent: Friday, April 27, 2018 11:52:00 AM
To: Scott Cain

Cc: gmo...@li...<mailto:gmo...@li...>
Subject: Re: [Gmod-ajax] Fw: ./setup.sh issues


No specific reason, was just follwing the JBrowse quick start guide http://jbrowse.org/code/JBrowse-1.14.0/docs/tutorial/index.html<https://urldefense.proofpoint.com/v2/url?u=http-3A__jbrowse.org_code_JBrowse-2D1.14.0_docs_tutorial_index.html&d=DwMFaQ&c=Pk_HpaIpE_jAoEC9PLIWoQ&r=tHmIv0YuoIPeACKiRmuf9tkl4ot_m-78ai1jalYUtZo&m=ZRWhaUFyclCWuHHrcb6XuPtdWtzGFkuDsVScf75KZg8&s=kT5q-_XUgRtbCgd4oslywdvhX5JA1PGuChAtmnPUNGU&e=>

I will try it with 1.14


Thanks,

Jonathan McMillan

________________________________
From: Scott Cain <sc...@sc...<mailto:sc...@sc...>>
Sent: Friday, April 27, 2018 11:33:21 AM
To: Jonathan McMillan
Cc: gmo...@li...<mailto:gmo...@li...>
Subject: Re: [Gmod-ajax] Fw: ./setup.sh issues

Hi Jonathan,

Much better--thanks!

It looks like you are trying to install a very old version of JBrowse, 1.8 (we are on 1.14) and it is failing trying to install SAMtools.  Is there a reason you want to use such an old version?

Scott


On Fri, Apr 27, 2018 at 12:08 PM, Jonathan McMillan <jon...@sl...<mailto:jon...@sl...>> wrote:



________________________________
From: Jon McMillan <jon...@ao...<mailto:jon...@ao...>>
Sent: Friday, April 27, 2018 11:06 AM
To: Jonathan McMillan
Subject: Re: [Gmod-ajax] ./setup.sh issues

Apologies for the sharepoint issues. Hope this works better.

Thanks,
Jonathan McMillan


-----Original Message-----
From: Jonathan McMillan <jon...@sl...<mailto:jon...@sl...>>
To: Jon McMillan <jon...@ao...<mailto:jon...@ao...>>
Sent: Fri, Apr 27, 2018 10:44 am
Subject: Fwd: [Gmod-ajax] ./setup.sh issues



Get Outlook for Android<https://urldefense.proofpoint.com/v2/url?u=https-3A__aka.ms_ghei36&d=DwMCaQ&c=Pk_HpaIpE_jAoEC9PLIWoQ&r=tHmIv0YuoIPeACKiRmuf9tkl4ot_m-78ai1jalYUtZo&m=BwD5ccOnH5jug6GXgCrIOTGVCnotmb9fPWUt_I8DQTA&s=PBf-VBKWIBSAIhwPw9nWL0l0KEsg6_Yl7cWoVexoLzY&e=>

________________________________
From: Robert Buels <rb...@gm...<mailto:rb...@gm...>>
Sent: Friday, April 27, 2018 10:27:54 AM
To: Jonathan McMillan
Cc: gmo...@li...<mailto:aj...@li...>
Subject: Re: [Gmod-ajax] ./setup.sh issues

Hi Jonathan,

Could you simply attach the files to the email or paste them into the body? Many of us do not have Microsoft accounts to log in to onedrive.




On Fri, Apr 27, 2018 at 8:02 AM Jonathan McMillan <jon...@sl...<mailto:jon...@sl...>> wrote:
Jonathan McMillan has shared OneDrive for Business files with you. To view them, click the links below.


<https://urldefense.proofpoint.com/v2/url?u=https-3A__sluedu-2Dmy.sharepoint.com_personal_jonathan-5Fmcmillan-5Fslu-5Fedu_Documents_Attachments_setup.log&d=DwMFaQ&c=Pk_HpaIpE_jAoEC9PLIWoQ&r=tHmIv0YuoIPeACKiRmuf9tkl4ot_m-78ai1jalYUtZo&m=WA7bUWjYcZJRlRdK9SqjMelunBgqpV2T1ivw6Wrv-dQ&s=sg6-NNJPT6yp3HZwoHznbVzJNRXz_9jTzw6q6qXTI54&e=>
[X]<https://urldefense.proofpoint.com/v2/url?u=https-3A__sluedu-2Dmy.sharepoint.com_personal_jonathan-5Fmcmillan-5Fslu-5Fedu_Documents_Attachments_setup.log&d=DwMFaQ&c=Pk_HpaIpE_jAoEC9PLIWoQ&r=tHmIv0YuoIPeACKiRmuf9tkl4ot_m-78ai1jalYUtZo&m=WA7bUWjYcZJRlRdK9SqjMelunBgqpV2T1ivw6Wrv-dQ&s=sg6-NNJPT6yp3HZwoHznbVzJNRXz_9jTzw6q6qXTI54&e=>

setup.log<https://urldefense.proofpoint.com/v2/url?u=https-3A__sluedu-2Dmy.sharepoint.com_personal_jonathan-5Fmcmillan-5Fslu-5Fedu_Documents_Attachments_setup.log&d=DwMFaQ&c=Pk_HpaIpE_jAoEC9PLIWoQ&r=tHmIv0YuoIPeACKiRmuf9tkl4ot_m-78ai1jalYUtZo&m=WA7bUWjYcZJRlRdK9SqjMelunBgqpV2T1ivw6Wrv-dQ&s=sg6-NNJPT6yp3HZwoHznbVzJNRXz_9jTzw6q6qXTI54&e=>

<https://urldefense.proofpoint.com/v2/url?u=https-3A__sluedu-2Dmy.sharepoint.com_personal_jonathan-5Fmcmillan-5Fslu-5Fedu_Documents_Attachments_setup-5Foutput.txt&d=DwMFaQ&c=Pk_HpaIpE_jAoEC9PLIWoQ&r=tHmIv0YuoIPeACKiRmuf9tkl4ot_m-78ai1jalYUtZo&m=WA7bUWjYcZJRlRdK9SqjMelunBgqpV2T1ivw6Wrv-dQ&s=Jq0Y1NAg9UY9i-9CJVdXdqgp_cDUnKR75F3m8Me3pfg&e=>
[X]<https://urldefense.proofpoint.com/v2/url?u=https-3A__sluedu-2Dmy.sharepoint.com_personal_jonathan-5Fmcmillan-5Fslu-5Fedu_Documents_Attachments_setup-5Foutput.txt&d=DwMFaQ&c=Pk_HpaIpE_jAoEC9PLIWoQ&r=tHmIv0YuoIPeACKiRmuf9tkl4ot_m-78ai1jalYUtZo&m=WA7bUWjYcZJRlRdK9SqjMelunBgqpV2T1ivw6Wrv-dQ&s=Jq0Y1NAg9UY9i-9CJVdXdqgp_cDUnKR75F3m8Me3pfg&e=>

setup_output.txt<https://urldefense.proofpoint.com/v2/url?u=https-3A__sluedu-2Dmy.sharepoint.com_personal_jonathan-5Fmcmillan-5Fslu-5Fedu_Documents_Attachments_setup-5Foutput.txt&d=DwMFaQ&c=Pk_HpaIpE_jAoEC9PLIWoQ&r=tHmIv0YuoIPeACKiRmuf9tkl4ot_m-78ai1jalYUtZo&m=WA7bUWjYcZJRlRdK9SqjMelunBgqpV2T1ivw6Wrv-dQ&s=Jq0Y1NAg9UY9i-9CJVdXdqgp_cDUnKR75F3m8Me3pfg&e=>



Hi,

I was having some issues with ./setup.sh

Here is the setup.log file and the txt file is the output from running ./setup.sh . An help is greatly appreciated!

Thanks,
Joanthan McMillan
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/<https://urldefense.proofpoint.com/v2/url?u=http-3A__gmod.org_&d=DwMFaQ&c=Pk_HpaIpE_jAoEC9PLIWoQ&r=tHmIv0YuoIPeACKiRmuf9tkl4ot_m-78ai1jalYUtZo&m=HRli8jHaIHMVdCKDPLv0IW0dfeJJPYQcvJs6mpNaEQc&s=UwH0VICRAUVx4vFSkKOuWEujt05Z7kukb4F92OMpUzE&e=>)                     216-392-3087
Ontario Institute for Cancer Research



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/<https://urldefense.proofpoint.com/v2/url?u=http-3A__gmod.org_&d=DwMFaQ&c=Pk_HpaIpE_jAoEC9PLIWoQ&r=tHmIv0YuoIPeACKiRmuf9tkl4ot_m-78ai1jalYUtZo&m=ZRWhaUFyclCWuHHrcb6XuPtdWtzGFkuDsVScf75KZg8&s=TiSJVixFjcZ_D1J6JbTy5PhdI7mN3DAVyBNE4kxX1Hg&e=>)                     216-392-3087
Ontario Institute for Cancer Research



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/<https://urldefense.proofpoint.com/v2/url?u=http-3A__gmod.org_&d=DwMFaQ&c=Pk_HpaIpE_jAoEC9PLIWoQ&r=tHmIv0YuoIPeACKiRmuf9tkl4ot_m-78ai1jalYUtZo&m=ZRWhaUFyclCWuHHrcb6XuPtdWtzGFkuDsVScf75KZg8&s=TiSJVixFjcZ_D1J6JbTy5PhdI7mN3DAVyBNE4kxX1Hg&e=>)                     216-392-3087
Ontario Institute for Cancer Research

Re: [Gmod-ajax] Fw: ./setup.sh issues

[Jonathan M. <jon...@sl...>]

Downloaded Nodejs and retried the download, seems to be a success! Thanks so much for the help today!


Thanks,

Jonathan McMillan

________________________________
From: Jonathan McMillan
Sent: Friday, April 27, 2018 3:37:53 PM
To: Scott Cain; Robert Buels; Eric Yao
Cc: gmo...@li...
Subject: Re: [Gmod-ajax] Fw: ./setup.sh issues


So I had been using curl to grab the zip file from github, trying to unzip files grabbed from curl would not unzip. Tried wget and worked first time!


Tried ./setup.sh again, which failed. This is the .log file, do I need to download node.js onto my machine in order to download JBrowse?

<https://drive.google.com/open?id=1nksTM4y3qCa2_k3IsGPs4EuWMK860DT3>https://drive.google.com/file/d/1nksTM4y3qCa2_k3IsGPs4EuWMK860DT3/view?usp=sharing

[https://lh6.googleusercontent.com/2ezWPRTpAPpp_x5RJrg0RwsidCtLosVJVrrQeyrfdC9kNXXRglJ_jSHyeOs=w1200-h630-p]<https://drive.google.com/file/d/1nksTM4y3qCa2_k3IsGPs4EuWMK860DT3/view?usp=sharing>

setup.log<https://drive.google.com/file/d/1nksTM4y3qCa2_k3IsGPs4EuWMK860DT3/view?usp=sharing>
drive.google.com

Thanks,

Jonathan McMillan

________________________________
From: Scott Cain <sc...@sc...>
Sent: Friday, April 27, 2018 2:42:15 PM
To: Jonathan McMillan; Robert Buels; Eric Yao
Cc: gmo...@li...
Subject: Re: [Gmod-ajax] Fw: ./setup.sh issues

And I just noticed there isn't a tar.gz file (there always used to be!)  Sorry about that; another thing I'd suggest is using a different browser or using something like curl or wget to retrieve it.


On Fri, Apr 27, 2018 at 3:40 PM, Scott Cain <sc...@sc...<mailto:sc...@sc...>> wrote:
Hi Jonathan,

Perhaps the download got truncated? I just downloaded 1.14.0.zip and it unzipped fine, ALTHOUGH (and this is directed at Rob and Eric), when I did the md5sum of the downloaded zip file it does not match the md5 sum reported on the website, which is a bit of a problem.  Could you guys check that out?

Back to Jonathan: if downloading the zip file doesn't work, perhaps you could use the tar.gz file instead?

Scott


On Fri, Apr 27, 2018 at 1:45 PM, Jonathan McMillan <jon...@sl...<mailto:jon...@sl...>> wrote:

Hey again,


So I have the zip file downloaded from the github repo. But now when I try to unzip the file in my webserver there seems to be an error.

This is the output from my machine.

[ec2-user@###### jbrowse]$ unzip JBrowse-1.14.0.zip
Archive:  JBrowse-1.14.0.zip
  End-of-central-directory signature not found.  Either this file is not
  a zipfile, or it constitutes one disk of a multi-part archive.  In the
  latter case the central directory and zipfile comment will be found on
  the last disk(s) of this archive.
unzip:  cannot find zipfile directory in one of JBrowse-1.14.0.zip or
        JBrowse-1.14.0.zip.zip, and cannot find JBrowse-1.14.0.zip.ZIP, period.

[ec2-user@###### jbrowse]$ file JBrowse-1.14.0.zip
JBrowse-1.14.0.zip: HTML document, ASCII text, with very long lines, with no line terminators

Thanks for all the help,

Jonathan McMillan

________________________________
From: Jonathan McMillan
Sent: Friday, April 27, 2018 11:52:00 AM
To: Scott Cain

Cc: gmo...@li...<mailto:gmo...@li...>
Subject: Re: [Gmod-ajax] Fw: ./setup.sh issues


No specific reason, was just follwing the JBrowse quick start guide http://jbrowse.org/code/JBrowse-1.14.0/docs/tutorial/index.html<https://urldefense.proofpoint.com/v2/url?u=http-3A__jbrowse.org_code_JBrowse-2D1.14.0_docs_tutorial_index.html&d=DwMFaQ&c=Pk_HpaIpE_jAoEC9PLIWoQ&r=tHmIv0YuoIPeACKiRmuf9tkl4ot_m-78ai1jalYUtZo&m=ZRWhaUFyclCWuHHrcb6XuPtdWtzGFkuDsVScf75KZg8&s=kT5q-_XUgRtbCgd4oslywdvhX5JA1PGuChAtmnPUNGU&e=>

I will try it with 1.14


Thanks,

Jonathan McMillan

________________________________
From: Scott Cain <sc...@sc...<mailto:sc...@sc...>>
Sent: Friday, April 27, 2018 11:33:21 AM
To: Jonathan McMillan
Cc: gmo...@li...<mailto:gmo...@li...>
Subject: Re: [Gmod-ajax] Fw: ./setup.sh issues

Hi Jonathan,

Much better--thanks!

It looks like you are trying to install a very old version of JBrowse, 1.8 (we are on 1.14) and it is failing trying to install SAMtools.  Is there a reason you want to use such an old version?

Scott


On Fri, Apr 27, 2018 at 12:08 PM, Jonathan McMillan <jon...@sl...<mailto:jon...@sl...>> wrote:



________________________________
From: Jon McMillan <jon...@ao...<mailto:jon...@ao...>>
Sent: Friday, April 27, 2018 11:06 AM
To: Jonathan McMillan
Subject: Re: [Gmod-ajax] ./setup.sh issues

Apologies for the sharepoint issues. Hope this works better.

Thanks,
Jonathan McMillan


-----Original Message-----
From: Jonathan McMillan <jon...@sl...<mailto:jon...@sl...>>
To: Jon McMillan <jon...@ao...<mailto:jon...@ao...>>
Sent: Fri, Apr 27, 2018 10:44 am
Subject: Fwd: [Gmod-ajax] ./setup.sh issues



Get Outlook for Android<https://urldefense.proofpoint.com/v2/url?u=https-3A__aka.ms_ghei36&d=DwMCaQ&c=Pk_HpaIpE_jAoEC9PLIWoQ&r=tHmIv0YuoIPeACKiRmuf9tkl4ot_m-78ai1jalYUtZo&m=BwD5ccOnH5jug6GXgCrIOTGVCnotmb9fPWUt_I8DQTA&s=PBf-VBKWIBSAIhwPw9nWL0l0KEsg6_Yl7cWoVexoLzY&e=>

________________________________
From: Robert Buels <rb...@gm...<mailto:rb...@gm...>>
Sent: Friday, April 27, 2018 10:27:54 AM
To: Jonathan McMillan
Cc: gmo...@li...<mailto:aj...@li...>
Subject: Re: [Gmod-ajax] ./setup.sh issues

Hi Jonathan,

Could you simply attach the files to the email or paste them into the body? Many of us do not have Microsoft accounts to log in to onedrive.




On Fri, Apr 27, 2018 at 8:02 AM Jonathan McMillan <jon...@sl...<mailto:jon...@sl...>> wrote:
Jonathan McMillan has shared OneDrive for Business files with you. To view them, click the links below.


<https://urldefense.proofpoint.com/v2/url?u=https-3A__sluedu-2Dmy.sharepoint.com_personal_jonathan-5Fmcmillan-5Fslu-5Fedu_Documents_Attachments_setup.log&d=DwMFaQ&c=Pk_HpaIpE_jAoEC9PLIWoQ&r=tHmIv0YuoIPeACKiRmuf9tkl4ot_m-78ai1jalYUtZo&m=WA7bUWjYcZJRlRdK9SqjMelunBgqpV2T1ivw6Wrv-dQ&s=sg6-NNJPT6yp3HZwoHznbVzJNRXz_9jTzw6q6qXTI54&e=>
[X]<https://urldefense.proofpoint.com/v2/url?u=https-3A__sluedu-2Dmy.sharepoint.com_personal_jonathan-5Fmcmillan-5Fslu-5Fedu_Documents_Attachments_setup.log&d=DwMFaQ&c=Pk_HpaIpE_jAoEC9PLIWoQ&r=tHmIv0YuoIPeACKiRmuf9tkl4ot_m-78ai1jalYUtZo&m=WA7bUWjYcZJRlRdK9SqjMelunBgqpV2T1ivw6Wrv-dQ&s=sg6-NNJPT6yp3HZwoHznbVzJNRXz_9jTzw6q6qXTI54&e=>

setup.log<https://urldefense.proofpoint.com/v2/url?u=https-3A__sluedu-2Dmy.sharepoint.com_personal_jonathan-5Fmcmillan-5Fslu-5Fedu_Documents_Attachments_setup.log&d=DwMFaQ&c=Pk_HpaIpE_jAoEC9PLIWoQ&r=tHmIv0YuoIPeACKiRmuf9tkl4ot_m-78ai1jalYUtZo&m=WA7bUWjYcZJRlRdK9SqjMelunBgqpV2T1ivw6Wrv-dQ&s=sg6-NNJPT6yp3HZwoHznbVzJNRXz_9jTzw6q6qXTI54&e=>

<https://urldefense.proofpoint.com/v2/url?u=https-3A__sluedu-2Dmy.sharepoint.com_personal_jonathan-5Fmcmillan-5Fslu-5Fedu_Documents_Attachments_setup-5Foutput.txt&d=DwMFaQ&c=Pk_HpaIpE_jAoEC9PLIWoQ&r=tHmIv0YuoIPeACKiRmuf9tkl4ot_m-78ai1jalYUtZo&m=WA7bUWjYcZJRlRdK9SqjMelunBgqpV2T1ivw6Wrv-dQ&s=Jq0Y1NAg9UY9i-9CJVdXdqgp_cDUnKR75F3m8Me3pfg&e=>
[X]<https://urldefense.proofpoint.com/v2/url?u=https-3A__sluedu-2Dmy.sharepoint.com_personal_jonathan-5Fmcmillan-5Fslu-5Fedu_Documents_Attachments_setup-5Foutput.txt&d=DwMFaQ&c=Pk_HpaIpE_jAoEC9PLIWoQ&r=tHmIv0YuoIPeACKiRmuf9tkl4ot_m-78ai1jalYUtZo&m=WA7bUWjYcZJRlRdK9SqjMelunBgqpV2T1ivw6Wrv-dQ&s=Jq0Y1NAg9UY9i-9CJVdXdqgp_cDUnKR75F3m8Me3pfg&e=>

setup_output.txt<https://urldefense.proofpoint.com/v2/url?u=https-3A__sluedu-2Dmy.sharepoint.com_personal_jonathan-5Fmcmillan-5Fslu-5Fedu_Documents_Attachments_setup-5Foutput.txt&d=DwMFaQ&c=Pk_HpaIpE_jAoEC9PLIWoQ&r=tHmIv0YuoIPeACKiRmuf9tkl4ot_m-78ai1jalYUtZo&m=WA7bUWjYcZJRlRdK9SqjMelunBgqpV2T1ivw6Wrv-dQ&s=Jq0Y1NAg9UY9i-9CJVdXdqgp_cDUnKR75F3m8Me3pfg&e=>



Hi,

I was having some issues with ./setup.sh

Here is the setup.log file and the txt file is the output from running ./setup.sh . An help is greatly appreciated!

Thanks,
Joanthan McMillan
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/<https://urldefense.proofpoint.com/v2/url?u=http-3A__gmod.org_&d=DwMFaQ&c=Pk_HpaIpE_jAoEC9PLIWoQ&r=tHmIv0YuoIPeACKiRmuf9tkl4ot_m-78ai1jalYUtZo&m=HRli8jHaIHMVdCKDPLv0IW0dfeJJPYQcvJs6mpNaEQc&s=UwH0VICRAUVx4vFSkKOuWEujt05Z7kukb4F92OMpUzE&e=>)                     216-392-3087
Ontario Institute for Cancer Research



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/<https://urldefense.proofpoint.com/v2/url?u=http-3A__gmod.org_&d=DwMFaQ&c=Pk_HpaIpE_jAoEC9PLIWoQ&r=tHmIv0YuoIPeACKiRmuf9tkl4ot_m-78ai1jalYUtZo&m=ZRWhaUFyclCWuHHrcb6XuPtdWtzGFkuDsVScf75KZg8&s=TiSJVixFjcZ_D1J6JbTy5PhdI7mN3DAVyBNE4kxX1Hg&e=>)                     216-392-3087
Ontario Institute for Cancer Research



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/<https://urldefense.proofpoint.com/v2/url?u=http-3A__gmod.org_&d=DwMFaQ&c=Pk_HpaIpE_jAoEC9PLIWoQ&r=tHmIv0YuoIPeACKiRmuf9tkl4ot_m-78ai1jalYUtZo&m=ZRWhaUFyclCWuHHrcb6XuPtdWtzGFkuDsVScf75KZg8&s=TiSJVixFjcZ_D1J6JbTy5PhdI7mN3DAVyBNE4kxX1Hg&e=>)                     216-392-3087
Ontario Institute for Cancer Research

Re: [Gmod-ajax] Fw: ./setup.sh issues

[Scott C. <sc...@sc...>]

And I just noticed there isn't a tar.gz file (there always used to be!)
Sorry about that; another thing I'd suggest is using a different browser or
using something like curl or wget to retrieve it.


On Fri, Apr 27, 2018 at 3:40 PM, Scott Cain <sc...@sc...> wrote:

> Hi Jonathan,
>
> Perhaps the download got truncated? I just downloaded 1.14.0.zip and it
> unzipped fine, ALTHOUGH (and this is directed at Rob and Eric), when I did
> the md5sum of the downloaded zip file it does not match the md5 sum
> reported on the website, which is a bit of a problem.  Could you guys check
> that out?
>
> Back to Jonathan: if downloading the zip file doesn't work, perhaps you
> could use the tar.gz file instead?
>
> Scott
>
>
> On Fri, Apr 27, 2018 at 1:45 PM, Jonathan McMillan <
> jon...@sl...> wrote:
>
>> Hey again,
>>
>>
>> So I have the zip file downloaded from the github repo. But now when I
>> try to unzip the file in my webserver there seems to be an error.
>>
>> This is the output from my machine.
>>
>> [ec2-user@###### jbrowse]$ unzip JBrowse-1.14.0.zip
>> Archive:  JBrowse-1.14.0.zip
>>   End-of-central-directory signature not found.  Either this file is not
>>   a zipfile, or it constitutes one disk of a multi-part archive.  In the
>>   latter case the central directory and zipfile comment will be found on
>>   the last disk(s) of this archive.
>> unzip:  cannot find zipfile directory in one of JBrowse-1.14.0.zip or
>>         JBrowse-1.14.0.zip.zip, and cannot find JBrowse-1.14.0.zip.ZIP,
>> period.
>>
>> [ec2-user@###### jbrowse]$ file JBrowse-1.14.0.zip
>> JBrowse-1.14.0.zip: HTML document, ASCII text, with very long lines, with
>> no line terminators
>>
>> Thanks for all the help,
>>
>> Jonathan McMillan
>> ------------------------------
>> *From:* Jonathan McMillan
>> *Sent:* Friday, April 27, 2018 11:52:00 AM
>> *To:* Scott Cain
>>
>> *Cc:* gmo...@li...
>> *Subject:* Re: [Gmod-ajax] Fw: ./setup.sh issues
>>
>>
>> No specific reason, was just follwing the JBrowse quick start guide
>> http://jbrowse.org/code/JBrowse-1.14.0/docs/tutorial/index.html
>>
>> I will try it with 1.14
>>
>>
>> Thanks,
>>
>> Jonathan McMillan
>> ------------------------------
>> *From:* Scott Cain <sc...@sc...>
>> *Sent:* Friday, April 27, 2018 11:33:21 AM
>> *To:* Jonathan McMillan
>> *Cc:* gmo...@li...
>> *Subject:* Re: [Gmod-ajax] Fw: ./setup.sh issues
>>
>> Hi Jonathan,
>>
>> Much better--thanks!
>>
>> It looks like you are trying to install a very old version of JBrowse,
>> 1.8 (we are on 1.14) and it is failing trying to install SAMtools.  Is
>> there a reason you want to use such an old version?
>>
>> Scott
>>
>>
>> On Fri, Apr 27, 2018 at 12:08 PM, Jonathan McMillan <
>> jon...@sl...> wrote:
>>
>>
>>
>>
>> ------------------------------
>> *From:* Jon McMillan <jon...@ao...>
>> *Sent:* Friday, April 27, 2018 11:06 AM
>> *To:* Jonathan McMillan
>> *Subject:* Re: [Gmod-ajax] ./setup.sh issues
>>
>> Apologies for the sharepoint issues. Hope this works better.
>>
>> Thanks,
>> Jonathan McMillan
>>
>>
>> -----Original Message-----
>> From: Jonathan McMillan <jon...@sl...>
>> To: Jon McMillan <jon...@ao...>
>> Sent: Fri, Apr 27, 2018 10:44 am
>> Subject: Fwd: [Gmod-ajax] ./setup.sh issues
>>
>>
>>
>> Get Outlook for Android
>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__aka.ms_ghei36&d=DwMCaQ&c=Pk_HpaIpE_jAoEC9PLIWoQ&r=tHmIv0YuoIPeACKiRmuf9tkl4ot_m-78ai1jalYUtZo&m=BwD5ccOnH5jug6GXgCrIOTGVCnotmb9fPWUt_I8DQTA&s=PBf-VBKWIBSAIhwPw9nWL0l0KEsg6_Yl7cWoVexoLzY&e=>
>>
>> ------------------------------
>> *From:* Robert Buels <rb...@gm...>
>> *Sent:* Friday, April 27, 2018 10:27:54 AM
>> *To:* Jonathan McMillan
>> *Cc:* gmo...@li...
>> *Subject:* Re: [Gmod-ajax] ./setup.sh issues
>>
>> Hi Jonathan,
>>
>> Could you simply attach the files to the email or paste them into the
>> body? Many of us do not have Microsoft accounts to log in to onedrive.
>>
>>
>>
>>
>> On Fri, Apr 27, 2018 at 8:02 AM Jonathan McMillan <
>> jon...@sl...> wrote:
>>
>> Jonathan McMillan has shared OneDrive for Business files with you. To
>> view them, click the links below.
>>
>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__sluedu-2Dmy.sharepoint.com_personal_jonathan-5Fmcmillan-5Fslu-5Fedu_Documents_Attachments_setup.log&d=DwMFaQ&c=Pk_HpaIpE_jAoEC9PLIWoQ&r=tHmIv0YuoIPeACKiRmuf9tkl4ot_m-78ai1jalYUtZo&m=WA7bUWjYcZJRlRdK9SqjMelunBgqpV2T1ivw6Wrv-dQ&s=sg6-NNJPT6yp3HZwoHznbVzJNRXz_9jTzw6q6qXTI54&e=>
>> setup.log
>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__sluedu-2Dmy.sharepoint.com_personal_jonathan-5Fmcmillan-5Fslu-5Fedu_Documents_Attachments_setup.log&d=DwMFaQ&c=Pk_HpaIpE_jAoEC9PLIWoQ&r=tHmIv0YuoIPeACKiRmuf9tkl4ot_m-78ai1jalYUtZo&m=WA7bUWjYcZJRlRdK9SqjMelunBgqpV2T1ivw6Wrv-dQ&s=sg6-NNJPT6yp3HZwoHznbVzJNRXz_9jTzw6q6qXTI54&e=>
>>
>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__sluedu-2Dmy.sharepoint.com_personal_jonathan-5Fmcmillan-5Fslu-5Fedu_Documents_Attachments_setup.log&d=DwMFaQ&c=Pk_HpaIpE_jAoEC9PLIWoQ&r=tHmIv0YuoIPeACKiRmuf9tkl4ot_m-78ai1jalYUtZo&m=WA7bUWjYcZJRlRdK9SqjMelunBgqpV2T1ivw6Wrv-dQ&s=sg6-NNJPT6yp3HZwoHznbVzJNRXz_9jTzw6q6qXTI54&e=>
>>
>>
>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__sluedu-2Dmy.sharepoint.com_personal_jonathan-5Fmcmillan-5Fslu-5Fedu_Documents_Attachments_setup-5Foutput.txt&d=DwMFaQ&c=Pk_HpaIpE_jAoEC9PLIWoQ&r=tHmIv0YuoIPeACKiRmuf9tkl4ot_m-78ai1jalYUtZo&m=WA7bUWjYcZJRlRdK9SqjMelunBgqpV2T1ivw6Wrv-dQ&s=Jq0Y1NAg9UY9i-9CJVdXdqgp_cDUnKR75F3m8Me3pfg&e=>
>> setup_output.txt
>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__sluedu-2Dmy.sharepoint.com_personal_jonathan-5Fmcmillan-5Fslu-5Fedu_Documents_Attachments_setup-5Foutput.txt&d=DwMFaQ&c=Pk_HpaIpE_jAoEC9PLIWoQ&r=tHmIv0YuoIPeACKiRmuf9tkl4ot_m-78ai1jalYUtZo&m=WA7bUWjYcZJRlRdK9SqjMelunBgqpV2T1ivw6Wrv-dQ&s=Jq0Y1NAg9UY9i-9CJVdXdqgp_cDUnKR75F3m8Me3pfg&e=>
>>
>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__sluedu-2Dmy.sharepoint.com_personal_jonathan-5Fmcmillan-5Fslu-5Fedu_Documents_Attachments_setup-5Foutput.txt&d=DwMFaQ&c=Pk_HpaIpE_jAoEC9PLIWoQ&r=tHmIv0YuoIPeACKiRmuf9tkl4ot_m-78ai1jalYUtZo&m=WA7bUWjYcZJRlRdK9SqjMelunBgqpV2T1ivw6Wrv-dQ&s=Jq0Y1NAg9UY9i-9CJVdXdqgp_cDUnKR75F3m8Me3pfg&e=>
>> Hi,
>>
>> I was having some issues with ./setup.sh
>>
>> Here is the setup.log file and the txt file is the output from running
>> ./setup.sh . An help is greatly appreciated!
>>
>> Thanks,
>> Joanthan McMillan
>> ------------------------------------------------------------
>> ------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__sdm.link_slashdot&d=DwMFaQ&c=Pk_HpaIpE_jAoEC9PLIWoQ&r=tHmIv0YuoIPeACKiRmuf9tkl4ot_m-78ai1jalYUtZo&m=WA7bUWjYcZJRlRdK9SqjMelunBgqpV2T1ivw6Wrv-dQ&s=JlMFpXK90-w3QuIk8KYb7xAQ2MVZDvKVeBVJmHARWaQ&e=>
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.sourceforge.net_lists_listinfo_gmod-2Dajax&d=DwMFaQ&c=Pk_HpaIpE_jAoEC9PLIWoQ&r=tHmIv0YuoIPeACKiRmuf9tkl4ot_m-78ai1jalYUtZo&m=WA7bUWjYcZJRlRdK9SqjMelunBgqpV2T1ivw6Wrv-dQ&s=kl-JevJ4UBXXIFbdpTwyqnubj-LLrkOIfW7XkSzWRX0&e=>
>>
>>
>> ------------------------------------------------------------
>> ------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__sdm.link_slashdot&d=DwMFaQ&c=Pk_HpaIpE_jAoEC9PLIWoQ&r=tHmIv0YuoIPeACKiRmuf9tkl4ot_m-78ai1jalYUtZo&m=HRli8jHaIHMVdCKDPLv0IW0dfeJJPYQcvJs6mpNaEQc&s=djC5tmHwZGmEK5jMGrlEFkEebPbACLpVykK9I0LeUao&e=>
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.sourceforge.net_lists_listinfo_gmod-2Dajax&d=DwMFaQ&c=Pk_HpaIpE_jAoEC9PLIWoQ&r=tHmIv0YuoIPeACKiRmuf9tkl4ot_m-78ai1jalYUtZo&m=HRli8jHaIHMVdCKDPLv0IW0dfeJJPYQcvJs6mpNaEQc&s=PdpbCK211WVSilNPsAoRfuZOjyXtmPG7cgw9-rAr4kI&e=>
>>
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain
>> dot net
>> GMOD Coordinator (http://gmod.org/
>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__gmod.org_&d=DwMFaQ&c=Pk_HpaIpE_jAoEC9PLIWoQ&r=tHmIv0YuoIPeACKiRmuf9tkl4ot_m-78ai1jalYUtZo&m=HRli8jHaIHMVdCKDPLv0IW0dfeJJPYQcvJs6mpNaEQc&s=UwH0VICRAUVx4vFSkKOuWEujt05Z7kukb4F92OMpUzE&e=>)
>>                    216-392-3087
>> Ontario Institute for Cancer Research
>>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain
> dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

Re: [Gmod-ajax] Fw: ./setup.sh issues

[Scott C. <sc...@sc...>]

Hi Jonathan,

Perhaps the download got truncated? I just downloaded 1.14.0.zip and it
unzipped fine, ALTHOUGH (and this is directed at Rob and Eric), when I did
the md5sum of the downloaded zip file it does not match the md5 sum
reported on the website, which is a bit of a problem.  Could you guys check
that out?

Back to Jonathan: if downloading the zip file doesn't work, perhaps you
could use the tar.gz file instead?

Scott


On Fri, Apr 27, 2018 at 1:45 PM, Jonathan McMillan <
jon...@sl...> wrote:

> Hey again,
>
>
> So I have the zip file downloaded from the github repo. But now when I try
> to unzip the file in my webserver there seems to be an error.
>
> This is the output from my machine.
>
> [ec2-user@###### jbrowse]$ unzip JBrowse-1.14.0.zip
> Archive:  JBrowse-1.14.0.zip
>   End-of-central-directory signature not found.  Either this file is not
>   a zipfile, or it constitutes one disk of a multi-part archive.  In the
>   latter case the central directory and zipfile comment will be found on
>   the last disk(s) of this archive.
> unzip:  cannot find zipfile directory in one of JBrowse-1.14.0.zip or
>         JBrowse-1.14.0.zip.zip, and cannot find JBrowse-1.14.0.zip.ZIP,
> period.
>
> [ec2-user@###### jbrowse]$ file JBrowse-1.14.0.zip
> JBrowse-1.14.0.zip: HTML document, ASCII text, with very long lines, with
> no line terminators
>
> Thanks for all the help,
>
> Jonathan McMillan
> ------------------------------
> *From:* Jonathan McMillan
> *Sent:* Friday, April 27, 2018 11:52:00 AM
> *To:* Scott Cain
>
> *Cc:* gmo...@li...
> *Subject:* Re: [Gmod-ajax] Fw: ./setup.sh issues
>
>
> No specific reason, was just follwing the JBrowse quick start guide
> http://jbrowse.org/code/JBrowse-1.14.0/docs/tutorial/index.html
>
> I will try it with 1.14
>
>
> Thanks,
>
> Jonathan McMillan
> ------------------------------
> *From:* Scott Cain <sc...@sc...>
> *Sent:* Friday, April 27, 2018 11:33:21 AM
> *To:* Jonathan McMillan
> *Cc:* gmo...@li...
> *Subject:* Re: [Gmod-ajax] Fw: ./setup.sh issues
>
> Hi Jonathan,
>
> Much better--thanks!
>
> It looks like you are trying to install a very old version of JBrowse, 1.8
> (we are on 1.14) and it is failing trying to install SAMtools.  Is there a
> reason you want to use such an old version?
>
> Scott
>
>
> On Fri, Apr 27, 2018 at 12:08 PM, Jonathan McMillan <
> jon...@sl...> wrote:
>
>
>
>
> ------------------------------
> *From:* Jon McMillan <jon...@ao...>
> *Sent:* Friday, April 27, 2018 11:06 AM
> *To:* Jonathan McMillan
> *Subject:* Re: [Gmod-ajax] ./setup.sh issues
>
> Apologies for the sharepoint issues. Hope this works better.
>
> Thanks,
> Jonathan McMillan
>
>
> -----Original Message-----
> From: Jonathan McMillan <jon...@sl...>
> To: Jon McMillan <jon...@ao...>
> Sent: Fri, Apr 27, 2018 10:44 am
> Subject: Fwd: [Gmod-ajax] ./setup.sh issues
>
>
>
> Get Outlook for Android
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__aka.ms_ghei36&d=DwMCaQ&c=Pk_HpaIpE_jAoEC9PLIWoQ&r=tHmIv0YuoIPeACKiRmuf9tkl4ot_m-78ai1jalYUtZo&m=BwD5ccOnH5jug6GXgCrIOTGVCnotmb9fPWUt_I8DQTA&s=PBf-VBKWIBSAIhwPw9nWL0l0KEsg6_Yl7cWoVexoLzY&e=>
>
> ------------------------------
> *From:* Robert Buels <rb...@gm...>
> *Sent:* Friday, April 27, 2018 10:27:54 AM
> *To:* Jonathan McMillan
> *Cc:* gmo...@li...
> *Subject:* Re: [Gmod-ajax] ./setup.sh issues
>
> Hi Jonathan,
>
> Could you simply attach the files to the email or paste them into the
> body? Many of us do not have Microsoft accounts to log in to onedrive.
>
>
>
>
> On Fri, Apr 27, 2018 at 8:02 AM Jonathan McMillan <
> jon...@sl...> wrote:
>
> Jonathan McMillan has shared OneDrive for Business files with you. To view
> them, click the links below.
>
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__sluedu-2Dmy.sharepoint.com_personal_jonathan-5Fmcmillan-5Fslu-5Fedu_Documents_Attachments_setup.log&d=DwMFaQ&c=Pk_HpaIpE_jAoEC9PLIWoQ&r=tHmIv0YuoIPeACKiRmuf9tkl4ot_m-78ai1jalYUtZo&m=WA7bUWjYcZJRlRdK9SqjMelunBgqpV2T1ivw6Wrv-dQ&s=sg6-NNJPT6yp3HZwoHznbVzJNRXz_9jTzw6q6qXTI54&e=>
> setup.log
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__sluedu-2Dmy.sharepoint.com_personal_jonathan-5Fmcmillan-5Fslu-5Fedu_Documents_Attachments_setup.log&d=DwMFaQ&c=Pk_HpaIpE_jAoEC9PLIWoQ&r=tHmIv0YuoIPeACKiRmuf9tkl4ot_m-78ai1jalYUtZo&m=WA7bUWjYcZJRlRdK9SqjMelunBgqpV2T1ivw6Wrv-dQ&s=sg6-NNJPT6yp3HZwoHznbVzJNRXz_9jTzw6q6qXTI54&e=>
>
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__sluedu-2Dmy.sharepoint.com_personal_jonathan-5Fmcmillan-5Fslu-5Fedu_Documents_Attachments_setup.log&d=DwMFaQ&c=Pk_HpaIpE_jAoEC9PLIWoQ&r=tHmIv0YuoIPeACKiRmuf9tkl4ot_m-78ai1jalYUtZo&m=WA7bUWjYcZJRlRdK9SqjMelunBgqpV2T1ivw6Wrv-dQ&s=sg6-NNJPT6yp3HZwoHznbVzJNRXz_9jTzw6q6qXTI54&e=>
>
>
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__sluedu-2Dmy.sharepoint.com_personal_jonathan-5Fmcmillan-5Fslu-5Fedu_Documents_Attachments_setup-5Foutput.txt&d=DwMFaQ&c=Pk_HpaIpE_jAoEC9PLIWoQ&r=tHmIv0YuoIPeACKiRmuf9tkl4ot_m-78ai1jalYUtZo&m=WA7bUWjYcZJRlRdK9SqjMelunBgqpV2T1ivw6Wrv-dQ&s=Jq0Y1NAg9UY9i-9CJVdXdqgp_cDUnKR75F3m8Me3pfg&e=>
> setup_output.txt
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__sluedu-2Dmy.sharepoint.com_personal_jonathan-5Fmcmillan-5Fslu-5Fedu_Documents_Attachments_setup-5Foutput.txt&d=DwMFaQ&c=Pk_HpaIpE_jAoEC9PLIWoQ&r=tHmIv0YuoIPeACKiRmuf9tkl4ot_m-78ai1jalYUtZo&m=WA7bUWjYcZJRlRdK9SqjMelunBgqpV2T1ivw6Wrv-dQ&s=Jq0Y1NAg9UY9i-9CJVdXdqgp_cDUnKR75F3m8Me3pfg&e=>
>
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__sluedu-2Dmy.sharepoint.com_personal_jonathan-5Fmcmillan-5Fslu-5Fedu_Documents_Attachments_setup-5Foutput.txt&d=DwMFaQ&c=Pk_HpaIpE_jAoEC9PLIWoQ&r=tHmIv0YuoIPeACKiRmuf9tkl4ot_m-78ai1jalYUtZo&m=WA7bUWjYcZJRlRdK9SqjMelunBgqpV2T1ivw6Wrv-dQ&s=Jq0Y1NAg9UY9i-9CJVdXdqgp_cDUnKR75F3m8Me3pfg&e=>
> Hi,
>
> I was having some issues with ./setup.sh
>
> Here is the setup.log file and the txt file is the output from running
> ./setup.sh . An help is greatly appreciated!
>
> Thanks,
> Joanthan McMillan
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
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> ------------------
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> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain
> dot net
> GMOD Coordinator (http://gmod.org/
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__gmod.org_&d=DwMFaQ&c=Pk_HpaIpE_jAoEC9PLIWoQ&r=tHmIv0YuoIPeACKiRmuf9tkl4ot_m-78ai1jalYUtZo&m=HRli8jHaIHMVdCKDPLv0IW0dfeJJPYQcvJs6mpNaEQc&s=UwH0VICRAUVx4vFSkKOuWEujt05Z7kukb4F92OMpUzE&e=>)
>                    216-392-3087
> Ontario Institute for Cancer Research
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research