[Gmod-ajax] Install on OSX Mavericks

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[Gmod-ajax] Install on OSX Mavericks

Ted Toal
I'm trying to install JBrowse on my Macbook running OSX Mavericks.  The quick installation process seemed to complete ok, but when I try to access it I get the page with this error:

However, JBrowse could not start, either because it has not yet been configured and loaded with data, or because of an error.

The JBrowse Configuration Guide says to run ./setup.sh without sudo, but I ran it with sudo.  I suppose this messed things up.  I removed the entire JBrowse-1.11.3 folder and re-unzipped and re-ran ./setup.sh, but the same error occurs.

I don't see any troubleshooting guide in the JBrowse Configuration Guide, nor any reference to a place to go that might describe troubleshooting.

I'm wondering if there are prerequisites I'm missing.  I didn't do any prerequisites installation.  I already have XCode installed so I have a C compiler.  The JBrowse Config Guide says to do this on Ubuntu:

sudo apt-get install zlib1g-dev libpng-dev libgd2-noxpm-dev build-essential

But since I don't have Ubuntu, I'm hesitant to just try that.

ttoal





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Re: Install on OSX Mavericks

Raymond Wan

Dear Ted,


Quoting Ted Toal <[hidden email]>:

> I'm trying to install JBrowse on my Macbook running OSX Mavericks.  The quick
> installation process seemed to complete ok, but when I try to access it I get
> the page with this error:
>
> However, JBrowse could not start, either because it has not yet been
> configured and loaded with data, or because of an error.


I don't use OSX myself, but you might want to look at the web server logs to see
if there are any helpful error messages.


> I don't see any troubleshooting guide in the JBrowse Configuration Guide, nor
> any reference to a place to go that might describe troubleshooting.


I'm not running the latest version, but in the version I am running, after I
unarchive the files, there is a file called INSTALL.  If you view that file, it
says:

For installation instructions, point your browser at
docs/tutorial/index.html in this directory.

If you view that file, there is a link that says "JBrowse Troubleshooting".
Have you done all this already?


> I'm wondering if there are prerequisites I'm missing.  I didn't do any
> prerequisites installation.  I already have XCode installed so I have a C
> compiler.  The JBrowse Config Guide says to do this on Ubuntu:


For OSX, the above document says,

"Use MacPorts, Fink, Homebrew, or another package manager to install a C++
compiler, libpng development headers, GD development headers, and Zlib
development headers."

So, it seems yes...

Ray




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Re: Install on OSX Mavericks

girlwithglasses
In reply to this post by Ted Toal
Hello Ted,

Have you already got Apache up and running on OS X Mavericks successfully? IIRC, it isn't turned on automatically and you'll need to do a little configuration work first.

Let us know what the situation is.

Thanks,
Amelia.


On Wed, Apr 30, 2014 at 8:56 AM, Ted Toal <[hidden email]> wrote:
I'm trying to install JBrowse on my Macbook running OSX Mavericks.  The quick installation process seemed to complete ok, but when I try to access it I get the page with this error:

However, JBrowse could not start, either because it has not yet been configured and loaded with data, or because of an error.

The JBrowse Configuration Guide says to run ./setup.sh without sudo, but I ran it with sudo.  I suppose this messed things up.  I removed the entire JBrowse-1.11.3 folder and re-unzipped and re-ran ./setup.sh, but the same error occurs.

I don't see any troubleshooting guide in the JBrowse Configuration Guide, nor any reference to a place to go that might describe troubleshooting.

I'm wondering if there are prerequisites I'm missing.  I didn't do any prerequisites installation.  I already have XCode installed so I have a C compiler.  The JBrowse Config Guide says to do this on Ubuntu:

sudo apt-get install zlib1g-dev libpng-dev libgd2-noxpm-dev build-essential

But since I don't have Ubuntu, I'm hesitant to just try that.

ttoal





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Re: Install on OSX Mavericks

Scott Cain
In reply to this post by Raymond Wan
Hi Ted,

You can also read the setup.log and look for errors.  I imagine there will be some :-)

I find the Mac OS just unixy enough to be familiar on the command line, but different enough to be a PITA, so I usually end up using AWS or VirtualBox and a linux distro.

Scott



On Wed, Apr 30, 2014 at 12:36 PM, Raymond Wan <[hidden email]> wrote:

Dear Ted,


Quoting Ted Toal <[hidden email]>:

> I'm trying to install JBrowse on my Macbook running OSX Mavericks.  The quick
> installation process seemed to complete ok, but when I try to access it I get
> the page with this error:
>
> However, JBrowse could not start, either because it has not yet been
> configured and loaded with data, or because of an error.


I don't use OSX myself, but you might want to look at the web server logs to see
if there are any helpful error messages.


> I don't see any troubleshooting guide in the JBrowse Configuration Guide, nor
> any reference to a place to go that might describe troubleshooting.


I'm not running the latest version, but in the version I am running, after I
unarchive the files, there is a file called INSTALL.  If you view that file, it
says:

For installation instructions, point your browser at
docs/tutorial/index.html in this directory.

If you view that file, there is a link that says "JBrowse Troubleshooting".
Have you done all this already?


> I'm wondering if there are prerequisites I'm missing.  I didn't do any
> prerequisites installation.  I already have XCode installed so I have a C
> compiler.  The JBrowse Config Guide says to do this on Ubuntu:


For OSX, the above document says,

"Use MacPorts, Fink, Homebrew, or another package manager to install a C++
compiler, libpng development headers, GD development headers, and Zlib
development headers."

So, it seems yes...

Ray




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Instantly run your Selenium tests across 300+ browser/OS combos.  Get
unparalleled scalability from the best Selenium testing platform available.
Simple to use. Nothing to install. Get started now for free."
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------------------------------------------------------------------------
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GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Instantly run your Selenium tests across 300+ browser/OS combos.  Get
unparalleled scalability from the best Selenium testing platform available.
Simple to use. Nothing to install. Get started now for free."
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Re: Install on OSX Mavericks

Ted Toal
In reply to this post by girlwithglasses
Hello Amelia,

Yes, I did get Apache up on and running on OS X Mavericks.  That part is working. 

ted

On Apr 30, 2014, at 11:09 AM, Amelia Ireland <[hidden email]> wrote:

Hello Ted,

Have you already got Apache up and running on OS X Mavericks successfully? IIRC, it isn't turned on automatically and you'll need to do a little configuration work first.

Let us know what the situation is.

Thanks,
Amelia.


On Wed, Apr 30, 2014 at 8:56 AM, Ted Toal <[hidden email]> wrote:
I'm trying to install JBrowse on my Macbook running OSX Mavericks.  The quick installation process seemed to complete ok, but when I try to access it I get the page with this error:

However, JBrowse could not start, either because it has not yet been configured and loaded with data, or because of an error.

The JBrowse Configuration Guide says to run ./setup.sh without sudo, but I ran it with sudo.  I suppose this messed things up.  I removed the entire JBrowse-1.11.3 folder and re-unzipped and re-ran ./setup.sh, but the same error occurs.

I don't see any troubleshooting guide in the JBrowse Configuration Guide, nor any reference to a place to go that might describe troubleshooting.

I'm wondering if there are prerequisites I'm missing.  I didn't do any prerequisites installation.  I already have XCode installed so I have a C compiler.  The JBrowse Config Guide says to do this on Ubuntu:

sudo apt-get install zlib1g-dev libpng-dev libgd2-noxpm-dev build-essential

But since I don't have Ubuntu, I'm hesitant to just try that.

ttoal





------------------------------------------------------------------------------
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Instantly run your Selenium tests across 300+ browser/OS combos.  Get
unparalleled scalability from the best Selenium testing platform available.
Simple to use. Nothing to install. Get started now for free."
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--
Amelia Ireland
GMOD Community Support
Generic Model Organism Database project
http://gmod.org || @gmodproject


--
Ted Toal, Graduate Student, [hidden email]
Brady Lab, UC Davis, Life Sciences 2243
One Shields Ave., Davis, CA  95616, ph: (530) 752-2537







------------------------------------------------------------------------------
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Instantly run your Selenium tests across 300+ browser/OS combos.  Get
unparalleled scalability from the best Selenium testing platform available.
Simple to use. Nothing to install. Get started now for free."
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Re: Install on OSX Mavericks

deepak.unni3
Hi Ted,

I also recently started using JBrowse.
In my case, even after installing all the dependencies, I still saw that message.

Have you tried clicking on 'Volvox test data here' link on the same page?
I have attached an image highlighting the link.

If JBrowse does load when you click this link then you should be all set.

If not, then as Scott mentioned, you should look at setup.log for any errors.

Best,

Deepak

On Wednesday, April 30, 2014 2:36 PM, Ted Toal <[hidden email]> wrote:
Hello Amelia,

Yes, I did get Apache up on and running on OS X Mavericks.  That part is working. 

ted

On Apr 30, 2014, at 11:09 AM, Amelia Ireland <[hidden email]> wrote:

Hello Ted,

Have you already got Apache up and running on OS X Mavericks successfully? IIRC, it isn't turned on automatically and you'll need to do a little configuration work first.

Let us know what the situation is.

Thanks,
Amelia.


On Wed, Apr 30, 2014 at 8:56 AM, Ted Toal <[hidden email]> wrote:
I'm trying to install JBrowse on my Macbook running OSX Mavericks.  The quick installation process seemed to complete ok, but when I try to access it I get the page with this error:

However, JBrowse could not start, either because it has not yet been configured and loaded with data, or because of an error.

The JBrowse Configuration Guide says to run ./setup.sh without sudo, but I ran it with sudo.  I suppose this messed things up.  I removed the entire JBrowse-1.11.3 folder and re-unzipped and re-ran ./setup.sh, but the same error occurs.

I don't see any troubleshooting guide in the JBrowse Configuration Guide, nor any reference to a place to go that might describe troubleshooting.

I'm wondering if there are prerequisites I'm missing.  I didn't do any prerequisites installation.  I already have XCode installed so I have a C compiler.  The JBrowse Config Guide says to do this on Ubuntu:

sudo apt-get install zlib1g-dev libpng-dev libgd2-noxpm-dev build-essential

But since I don't have Ubuntu, I'm hesitant to just try that.

ttoal





------------------------------------------------------------------------------
"Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
Instantly run your Selenium tests across 300+ browser/OS combos.  Get
unparalleled scalability from the best Selenium testing platform available.
Simple to use. Nothing to install. Get started now for free."
http://p.sf.net/sfu/SauceLabs
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax



--
Amelia Ireland
GMOD Community Support
Generic Model Organism Database project
http://gmod.org || @gmodproject


--
Ted Toal, Graduate Student, [hidden email]
Brady Lab, UC Davis, Life Sciences 2243
One Shields Ave., Davis, CA  95616, ph: (530) 752-2537







------------------------------------------------------------------------------
"Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
Instantly run your Selenium tests across 300+ browser/OS combos.  Get
unparalleled scalability from the best Selenium testing platform available.
Simple to use. Nothing to install. Get started now for free."
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Instantly run your Selenium tests across 300+ browser/OS combos.  Get
unparalleled scalability from the best Selenium testing platform available.
Simple to use. Nothing to install. Get started now for free."
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Re: Install on OSX Mavericks

Ted Toal
In reply to this post by Scott Cain
Thanks Ray and Scott.  Setup.log shows that libpng was missing and caused an error.  So, I tried installing it with MacPorts, then with fink.  I also tried installing the other packages shown in the  JBrowse Troubleshooting web page Ray pointed to.  So far no luck.  I see that the package names actually change between different versions of Linux.  So, I don't even know WHICH packages I might need, except that presumably their names would be SIMILAR to the names shown for Ubuntu (e.g. libpng-dev) and Red Hat (e.g. libpng-devel).  "fink list png" shows the list below on OSX, and nothing with "dev" in the name appears.  So, maybe there is no libpng development package for OSX?  Maybe JBrowse cannot be run on OSX?  Similarly for the zlib and gd packages.

Ted


     bmp2png                             1.62-3     
     gif2png                             2.5.8-1    
     libglpng1                           1.45-3     
     libglpng1-shlibs                    1.45-3     
     libpng14                            1.4.12-1   
     libpng14-shlibs                     1.4.12-1   
(i)  libpng15                            1.5.17-1   
     libpng15-32bit                      1.5.17-2   
     libpng15-32bit-shlibs               1.5.17-2   
(i)  libpng15-shlibs                     1.5.17-1   
     libpng16                            1.6.8-1    
     libpng16-32bit                      1.6.8-1    
     libpng16-32bit-shlibs               1.6.8-1    
     libpng16-shlibs                     1.6.8-1    
     libpng3-shlibs                      1:1.2.50-2 
     optipng                             0.6.3-1    
     pngcrush                            1.7.16-1   
     pngnq                               1.1-2      
 i   system-pkgconfig-cairo-png          1.12.14-1  
 i   system-pkgconfig-libpng             1.5.17-1   
 i   system-pkgconfig-libpng15           1.5.17-1   
     web2png                             2.5.8-1    



On Apr 30, 2014, at 11:13 AM, Scott Cain <[hidden email]> wrote:

Hi Ted,

You can also read the setup.log and look for errors.  I imagine there will be some :-)

I find the Mac OS just unixy enough to be familiar on the command line, but different enough to be a PITA, so I usually end up using AWS or VirtualBox and a linux distro.

Scott



On Wed, Apr 30, 2014 at 12:36 PM, Raymond Wan <[hidden email]> wrote:

Dear Ted,


Quoting Ted Toal <[hidden email]>:

> I'm trying to install JBrowse on my Macbook running OSX Mavericks.  The quick
> installation process seemed to complete ok, but when I try to access it I get
> the page with this error:
>
> However, JBrowse could not start, either because it has not yet been
> configured and loaded with data, or because of an error.


I don't use OSX myself, but you might want to look at the web server logs to see
if there are any helpful error messages.


> I don't see any troubleshooting guide in the JBrowse Configuration Guide, nor
> any reference to a place to go that might describe troubleshooting.


I'm not running the latest version, but in the version I am running, after I
unarchive the files, there is a file called INSTALL.  If you view that file, it
says:

For installation instructions, point your browser at
docs/tutorial/index.html in this directory.

If you view that file, there is a link that says "JBrowse Troubleshooting".
Have you done all this already?


> I'm wondering if there are prerequisites I'm missing.  I didn't do any
> prerequisites installation.  I already have XCode installed so I have a C
> compiler.  The JBrowse Config Guide says to do this on Ubuntu:


For OSX, the above document says,

"Use MacPorts, Fink, Homebrew, or another package manager to install a C++
compiler, libpng development headers, GD development headers, and Zlib
development headers."

So, it seems yes...

Ray




-------------------------------------------------
This e-mail is sent by CUHK WebMail http://webmail.cuhk.edu.hk


------------------------------------------------------------------------------
"Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
Instantly run your Selenium tests across 300+ browser/OS combos.  Get
unparalleled scalability from the best Selenium testing platform available.
Simple to use. Nothing to install. Get started now for free."
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

--
Ted Toal, Graduate Student, [hidden email]
Brady Lab, UC Davis, Life Sciences 2243
One Shields Ave., Davis, CA  95616, ph: (530) 752-2537







------------------------------------------------------------------------------
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Instantly run your Selenium tests across 300+ browser/OS combos.  Get
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Simple to use. Nothing to install. Get started now for free."
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Re: Install on OSX Mavericks

Ted Toal
In reply to this post by deepak.unni3
Yes, I have clicked on that link, and it does not work.  There are basic dependencies not yet installed.  I'm unable to install something called "expat", which seems to be a dependency of other required packages, and apparently this won't install because of a mixup somewhere in version numbers, with expat-2.1.0 getting mixed up with expat-2.0.1.  My frustration level is rising, it is beginning to feel like doing something on a Windows machine instead of a Mac.  I've spent way too much time on it.  I was hoping JBrowse would be a quick, easy, straightforward install that I could recommend to colleagues, and begin using it in my lab.  But I guess not.

ted

On Apr 30, 2014, at 12:42 PM, Deepak Unni <[hidden email]> wrote:

> Hi Ted,
>
> I also recently started using JBrowse.
> In my case, even after installing all the dependencies, I still saw that message.
>
> Have you tried clicking on 'Volvox test data here' link on the same page?
> I have attached an image highlighting the link.
>
> If JBrowse does load when you click this link then you should be all set.
>
> If not, then as Scott mentioned, you should look at setup.log for any errors.
>
> Best,
>
> Deepak
>
> On Wednesday, April 30, 2014 2:36 PM, Ted Toal <[hidden email]> wrote:
> Hello Amelia,
>
> Yes, I did get Apache up on and running on OS X Mavericks.  That part is working.
>
> ted
>
> On Apr 30, 2014, at 11:09 AM, Amelia Ireland <[hidden email]> wrote:
>
>> Hello Ted,
>>
>> Have you already got Apache up and running on OS X Mavericks successfully? IIRC, it isn't turned on automatically and you'll need to do a little configuration work first.
>>
>> Let us know what the situation is.
>>
>> Thanks,
>> Amelia.
>>
>>
>> On Wed, Apr 30, 2014 at 8:56 AM, Ted Toal <[hidden email]> wrote:
>> I'm trying to install JBrowse on my Macbook running OSX Mavericks.  The quick installation process seemed to complete ok, but when I try to access it I get the page with this error:
>>
>> However, JBrowse could not start, either because it has not yet been configured and loaded with data, or because of an error.
>>
>> The JBrowse Configuration Guide says to run ./setup.sh without sudo, but I ran it with sudo.  I suppose this messed things up.  I removed the entire JBrowse-1.11.3 folder and re-unzipped and re-ran ./setup.sh, but the same error occurs.
>>
>> I don't see any troubleshooting guide in the JBrowse Configuration Guide, nor any reference to a place to go that might describe troubleshooting.
>>
>> I'm wondering if there are prerequisites I'm missing.  I didn't do any prerequisites installation.  I already have XCode installed so I have a C compiler.  The JBrowse Config Guide says to do this on Ubuntu:
>>
>> sudo apt-get install zlib1g-dev libpng-dev libgd2-noxpm-dev build-essential
>>
>> But since I don't have Ubuntu, I'm hesitant to just try that.
>>
>> ttoal
>>
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
>> Instantly run your Selenium tests across 300+ browser/OS combos.  Get
>> unparalleled scalability from the best Selenium testing platform available.
>> Simple to use. Nothing to install. Get started now for free."
>> http://p.sf.net/sfu/SauceLabs
>> _______________________________________________
>> Gmod-ajax mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>>
>>
>> --
>> Amelia Ireland
>> GMOD Community Support
>> Generic Model Organism Database project
>> http://gmod.org || @gmodproject
>>
>
> --
> Ted Toal, Graduate Student, [hidden email]
> Brady Lab, UC Davis, Life Sciences 2243
> One Shields Ave., Davis, CA  95616, ph: (530) 752-2537
>
>
>
>
>
>
>
> ------------------------------------------------------------------------------
> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
> Instantly run your Selenium tests across 300+ browser/OS combos.  Get
> unparalleled scalability from the best Selenium testing platform available.
> Simple to use. Nothing to install. Get started now for free."
> http://p.sf.net/sfu/SauceLabs
>
> _______________________________________________
> Gmod-ajax mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
>
> <JBrowse.png>

--
Ted Toal, Graduate Student, [hidden email]
Brady Lab, UC Davis, Life Sciences 2243
One Shields Ave., Davis, CA  95616, ph: (530) 752-2537







------------------------------------------------------------------------------
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Instantly run your Selenium tests across 300+ browser/OS combos.  Get
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Simple to use. Nothing to install. Get started now for free."
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Re: Install on OSX Mavericks

girlwithglasses
Hi Ted,

You could try using GMOD in the Cloud, which is a virtual machine image in the Amazon Compute Cloud with JBrowse (plus other GMOD software) already set up on it. It takes very little time to get GMOD in the Cloud up and running, and you can run JBrowse on a "micro" instance because it's basically the browser that does all the work.

There is more information here:


This might be the quickest and easiest way to get JBrowse running if installing the dependencies on OS X is proving to be a nuisance.

Thanks,
Amelia.


On Wed, Apr 30, 2014 at 1:36 PM, Ted Toal <[hidden email]> wrote:
Yes, I have clicked on that link, and it does not work.  There are basic dependencies not yet installed.  I'm unable to install something called "expat", which seems to be a dependency of other required packages, and apparently this won't install because of a mixup somewhere in version numbers, with expat-2.1.0 getting mixed up with expat-2.0.1.  My frustration level is rising, it is beginning to feel like doing something on a Windows machine instead of a Mac.  I've spent way too much time on it.  I was hoping JBrowse would be a quick, easy, straightforward install that I could recommend to colleagues, and begin using it in my lab.  But I guess not.

ted

On Apr 30, 2014, at 12:42 PM, Deepak Unni <[hidden email]> wrote:

> Hi Ted,
>
> I also recently started using JBrowse.
> In my case, even after installing all the dependencies, I still saw that message.
>
> Have you tried clicking on 'Volvox test data here' link on the same page?
> I have attached an image highlighting the link.
>
> If JBrowse does load when you click this link then you should be all set.
>
> If not, then as Scott mentioned, you should look at setup.log for any errors.
>
> Best,
>
> Deepak
>
> On Wednesday, April 30, 2014 2:36 PM, Ted Toal <[hidden email]> wrote:
> Hello Amelia,
>
> Yes, I did get Apache up on and running on OS X Mavericks.  That part is working.
>
> ted
>
> On Apr 30, 2014, at 11:09 AM, Amelia Ireland <[hidden email]> wrote:
>
>> Hello Ted,
>>
>> Have you already got Apache up and running on OS X Mavericks successfully? IIRC, it isn't turned on automatically and you'll need to do a little configuration work first.
>>
>> Let us know what the situation is.
>>
>> Thanks,
>> Amelia.
>>
>>
>> On Wed, Apr 30, 2014 at 8:56 AM, Ted Toal <[hidden email]> wrote:
>> I'm trying to install JBrowse on my Macbook running OSX Mavericks.  The quick installation process seemed to complete ok, but when I try to access it I get the page with this error:
>>
>> However, JBrowse could not start, either because it has not yet been configured and loaded with data, or because of an error.
>>
>> The JBrowse Configuration Guide says to run ./setup.sh without sudo, but I ran it with sudo.  I suppose this messed things up.  I removed the entire JBrowse-1.11.3 folder and re-unzipped and re-ran ./setup.sh, but the same error occurs.
>>
>> I don't see any troubleshooting guide in the JBrowse Configuration Guide, nor any reference to a place to go that might describe troubleshooting.
>>
>> I'm wondering if there are prerequisites I'm missing.  I didn't do any prerequisites installation.  I already have XCode installed so I have a C compiler.  The JBrowse Config Guide says to do this on Ubuntu:
>>
>> sudo apt-get install zlib1g-dev libpng-dev libgd2-noxpm-dev build-essential
>>
>> But since I don't have Ubuntu, I'm hesitant to just try that.
>>
>> ttoal
>>
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
>> Instantly run your Selenium tests across 300+ browser/OS combos.  Get
>> unparalleled scalability from the best Selenium testing platform available.
>> Simple to use. Nothing to install. Get started now for free."
>> http://p.sf.net/sfu/SauceLabs
>> _______________________________________________
>> Gmod-ajax mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>>
>>
>> --
>> Amelia Ireland
>> GMOD Community Support
>> Generic Model Organism Database project
>> http://gmod.org || @gmodproject
>>
>
> --
> Ted Toal, Graduate Student, [hidden email]
> Brady Lab, UC Davis, Life Sciences 2243
> One Shields Ave., Davis, CA  95616, ph: <a href="tel:%28530%29%20752-2537" value="+15307522537">(530) 752-2537
>
>
>
>
>
>
>
> ------------------------------------------------------------------------------
> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
> Instantly run your Selenium tests across 300+ browser/OS combos.  Get
> unparalleled scalability from the best Selenium testing platform available.
> Simple to use. Nothing to install. Get started now for free."
> http://p.sf.net/sfu/SauceLabs
>
> _______________________________________________
> Gmod-ajax mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
>
> <JBrowse.png>

--
Ted Toal, Graduate Student, [hidden email]
Brady Lab, UC Davis, Life Sciences 2243
One Shields Ave., Davis, CA  95616, ph: <a href="tel:%28530%29%20752-2537" value="+15307522537">(530) 752-2537









--
Amelia Ireland
GMOD Community Support
Generic Model Organism Database project
http://gmod.org || @gmodproject


------------------------------------------------------------------------------
"Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
Instantly run your Selenium tests across 300+ browser/OS combos.  Get
unparalleled scalability from the best Selenium testing platform available.
Simple to use. Nothing to install. Get started now for free."
http://p.sf.net/sfu/SauceLabs
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Re: Install on OSX Mavericks

Ted Toal
Thanks, Amelia.  But I want to be able to browse gigabytes of .bam files among other things.  That probably won't work.  I would also like to be able to install basically the entire Tomato genome on it with multiple tracks, plus some of our lab tracks.  Sol Genomics runs a gbrowse tomato browser with custom track support, but when I tried uploading it failed, and they told me they support only very small custom tracks.  Would the Cloud version support what I need?

ted

On Apr 30, 2014, at 2:18 PM, Amelia Ireland <[hidden email]> wrote:

Hi Ted,

You could try using GMOD in the Cloud, which is a virtual machine image in the Amazon Compute Cloud with JBrowse (plus other GMOD software) already set up on it. It takes very little time to get GMOD in the Cloud up and running, and you can run JBrowse on a "micro" instance because it's basically the browser that does all the work.

There is more information here:


This might be the quickest and easiest way to get JBrowse running if installing the dependencies on OS X is proving to be a nuisance.

Thanks,
Amelia.


On Wed, Apr 30, 2014 at 1:36 PM, Ted Toal <[hidden email]> wrote:
Yes, I have clicked on that link, and it does not work.  There are basic dependencies not yet installed.  I'm unable to install something called "expat", which seems to be a dependency of other required packages, and apparently this won't install because of a mixup somewhere in version numbers, with expat-2.1.0 getting mixed up with expat-2.0.1.  My frustration level is rising, it is beginning to feel like doing something on a Windows machine instead of a Mac.  I've spent way too much time on it.  I was hoping JBrowse would be a quick, easy, straightforward install that I could recommend to colleagues, and begin using it in my lab.  But I guess not.

ted

On Apr 30, 2014, at 12:42 PM, Deepak Unni <[hidden email]> wrote:

> Hi Ted,
>
> I also recently started using JBrowse.
> In my case, even after installing all the dependencies, I still saw that message.
>
> Have you tried clicking on 'Volvox test data here' link on the same page?
> I have attached an image highlighting the link.
>
> If JBrowse does load when you click this link then you should be all set.
>
> If not, then as Scott mentioned, you should look at setup.log for any errors.
>
> Best,
>
> Deepak
>
> On Wednesday, April 30, 2014 2:36 PM, Ted Toal <[hidden email]> wrote:
> Hello Amelia,
>
> Yes, I did get Apache up on and running on OS X Mavericks.  That part is working.
>
> ted
>
> On Apr 30, 2014, at 11:09 AM, Amelia Ireland <[hidden email]> wrote:
>
>> Hello Ted,
>>
>> Have you already got Apache up and running on OS X Mavericks successfully? IIRC, it isn't turned on automatically and you'll need to do a little configuration work first.
>>
>> Let us know what the situation is.
>>
>> Thanks,
>> Amelia.
>>
>>
>> On Wed, Apr 30, 2014 at 8:56 AM, Ted Toal <[hidden email]> wrote:
>> I'm trying to install JBrowse on my Macbook running OSX Mavericks.  The quick installation process seemed to complete ok, but when I try to access it I get the page with this error:
>>
>> However, JBrowse could not start, either because it has not yet been configured and loaded with data, or because of an error.
>>
>> The JBrowse Configuration Guide says to run ./setup.sh without sudo, but I ran it with sudo.  I suppose this messed things up.  I removed the entire JBrowse-1.11.3 folder and re-unzipped and re-ran ./setup.sh, but the same error occurs.
>>
>> I don't see any troubleshooting guide in the JBrowse Configuration Guide, nor any reference to a place to go that might describe troubleshooting.
>>
>> I'm wondering if there are prerequisites I'm missing.  I didn't do any prerequisites installation.  I already have XCode installed so I have a C compiler.  The JBrowse Config Guide says to do this on Ubuntu:
>>
>> sudo apt-get install zlib1g-dev libpng-dev libgd2-noxpm-dev build-essential
>>
>> But since I don't have Ubuntu, I'm hesitant to just try that.
>>
>> ttoal
>>
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
>> Instantly run your Selenium tests across 300+ browser/OS combos.  Get
>> unparalleled scalability from the best Selenium testing platform available.
>> Simple to use. Nothing to install. Get started now for free."
>> http://p.sf.net/sfu/SauceLabs
>> _______________________________________________
>> Gmod-ajax mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>>
>>
>> --
>> Amelia Ireland
>> GMOD Community Support
>> Generic Model Organism Database project
>> http://gmod.org || @gmodproject
>>
>
> --
> Ted Toal, Graduate Student, [hidden email]
> Brady Lab, UC Davis, Life Sciences 2243
> One Shields Ave., Davis, CA  95616, ph: <a href="tel:%28530%29%20752-2537" value="+15307522537">(530) 752-2537
>
>
>
>
>
>
>
> ------------------------------------------------------------------------------
> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
> Instantly run your Selenium tests across 300+ browser/OS combos.  Get
> unparalleled scalability from the best Selenium testing platform available.
> Simple to use. Nothing to install. Get started now for free."
> http://p.sf.net/sfu/SauceLabs
>
> _______________________________________________
> Gmod-ajax mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
>
> <JBrowse.png>

--
Ted Toal, Graduate Student, [hidden email]
Brady Lab, UC Davis, Life Sciences 2243
One Shields Ave., Davis, CA  95616, ph: <a href="tel:%28530%29%20752-2537" value="+15307522537">(530) 752-2537









--
Amelia Ireland
GMOD Community Support
Generic Model Organism Database project
http://gmod.org || @gmodproject


--
Ted Toal, Graduate Student, [hidden email]
Brady Lab, UC Davis, Life Sciences 2243
One Shields Ave., Davis, CA  95616, ph: (530) 752-2537







------------------------------------------------------------------------------
"Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
Instantly run your Selenium tests across 300+ browser/OS combos.  Get
unparalleled scalability from the best Selenium testing platform available.
Simple to use. Nothing to install. Get started now for free."
http://p.sf.net/sfu/SauceLabs
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Re: Install on OSX Mavericks

Scott Cain
Hi Ted,

Actually, that probably would work pretty well: you'd need to get the GFF for tomato from SGN and process it (which you would have had to do for your local install anyway), and once that processing is done, you could probably run the JBrowse server as a "micro" machine, which are free to run for the first year you have your account.  I don't think you could do the processing on a micro machine because they are pretty limited in CPU and memory.

For JBrowse, the size of the bam files doesn't matter, because you don't need to upload them if you're the only person using them: JBrowse will use the BAM files directly from your computer without uploading them (so it's pretty fast too).

Scott



On Wed, Apr 30, 2014 at 5:29 PM, Ted Toal <[hidden email]> wrote:
Thanks, Amelia.  But I want to be able to browse gigabytes of .bam files among other things.  That probably won't work.  I would also like to be able to install basically the entire Tomato genome on it with multiple tracks, plus some of our lab tracks.  Sol Genomics runs a gbrowse tomato browser with custom track support, but when I tried uploading it failed, and they told me they support only very small custom tracks.  Would the Cloud version support what I need?

ted

On Apr 30, 2014, at 2:18 PM, Amelia Ireland <[hidden email]> wrote:

Hi Ted,

You could try using GMOD in the Cloud, which is a virtual machine image in the Amazon Compute Cloud with JBrowse (plus other GMOD software) already set up on it. It takes very little time to get GMOD in the Cloud up and running, and you can run JBrowse on a "micro" instance because it's basically the browser that does all the work.

There is more information here:


This might be the quickest and easiest way to get JBrowse running if installing the dependencies on OS X is proving to be a nuisance.

Thanks,
Amelia.


On Wed, Apr 30, 2014 at 1:36 PM, Ted Toal <[hidden email]> wrote:
Yes, I have clicked on that link, and it does not work.  There are basic dependencies not yet installed.  I'm unable to install something called "expat", which seems to be a dependency of other required packages, and apparently this won't install because of a mixup somewhere in version numbers, with expat-2.1.0 getting mixed up with expat-2.0.1.  My frustration level is rising, it is beginning to feel like doing something on a Windows machine instead of a Mac.  I've spent way too much time on it.  I was hoping JBrowse would be a quick, easy, straightforward install that I could recommend to colleagues, and begin using it in my lab.  But I guess not.

ted

On Apr 30, 2014, at 12:42 PM, Deepak Unni <[hidden email]> wrote:

> Hi Ted,
>
> I also recently started using JBrowse.
> In my case, even after installing all the dependencies, I still saw that message.
>
> Have you tried clicking on 'Volvox test data here' link on the same page?
> I have attached an image highlighting the link.
>
> If JBrowse does load when you click this link then you should be all set.
>
> If not, then as Scott mentioned, you should look at setup.log for any errors.
>
> Best,
>
> Deepak
>
> On Wednesday, April 30, 2014 2:36 PM, Ted Toal <[hidden email]> wrote:
> Hello Amelia,
>
> Yes, I did get Apache up on and running on OS X Mavericks.  That part is working.
>
> ted
>
> On Apr 30, 2014, at 11:09 AM, Amelia Ireland <[hidden email]> wrote:
>
>> Hello Ted,
>>
>> Have you already got Apache up and running on OS X Mavericks successfully? IIRC, it isn't turned on automatically and you'll need to do a little configuration work first.
>>
>> Let us know what the situation is.
>>
>> Thanks,
>> Amelia.
>>
>>
>> On Wed, Apr 30, 2014 at 8:56 AM, Ted Toal <[hidden email]> wrote:
>> I'm trying to install JBrowse on my Macbook running OSX Mavericks.  The quick installation process seemed to complete ok, but when I try to access it I get the page with this error:
>>
>> However, JBrowse could not start, either because it has not yet been configured and loaded with data, or because of an error.
>>
>> The JBrowse Configuration Guide says to run ./setup.sh without sudo, but I ran it with sudo.  I suppose this messed things up.  I removed the entire JBrowse-1.11.3 folder and re-unzipped and re-ran ./setup.sh, but the same error occurs.
>>
>> I don't see any troubleshooting guide in the JBrowse Configuration Guide, nor any reference to a place to go that might describe troubleshooting.
>>
>> I'm wondering if there are prerequisites I'm missing.  I didn't do any prerequisites installation.  I already have XCode installed so I have a C compiler.  The JBrowse Config Guide says to do this on Ubuntu:
>>
>> sudo apt-get install zlib1g-dev libpng-dev libgd2-noxpm-dev build-essential
>>
>> But since I don't have Ubuntu, I'm hesitant to just try that.
>>
>> ttoal
>>
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
>> Instantly run your Selenium tests across 300+ browser/OS combos.  Get
>> unparalleled scalability from the best Selenium testing platform available.
>> Simple to use. Nothing to install. Get started now for free."
>> http://p.sf.net/sfu/SauceLabs
>> _______________________________________________
>> Gmod-ajax mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>>
>>
>> --
>> Amelia Ireland
>> GMOD Community Support
>> Generic Model Organism Database project
>> http://gmod.org || @gmodproject
>>
>
> --
> Ted Toal, Graduate Student, [hidden email]
> Brady Lab, UC Davis, Life Sciences 2243
> One Shields Ave., Davis, CA  95616, ph: <a href="tel:%28530%29%20752-2537" value="+15307522537" target="_blank">(530) 752-2537
>
>
>
>
>
>
>
> ------------------------------------------------------------------------------
> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
> Instantly run your Selenium tests across 300+ browser/OS combos.  Get
> unparalleled scalability from the best Selenium testing platform available.
> Simple to use. Nothing to install. Get started now for free."
> http://p.sf.net/sfu/SauceLabs
>
> _______________________________________________
> Gmod-ajax mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
>
> <JBrowse.png>

--
Ted Toal, Graduate Student, [hidden email]
Brady Lab, UC Davis, Life Sciences 2243
One Shields Ave., Davis, CA  95616, ph: <a href="tel:%28530%29%20752-2537" value="+15307522537" target="_blank">(530) 752-2537









--
Amelia Ireland
GMOD Community Support
Generic Model Organism Database project
http://gmod.org || @gmodproject


--
Ted Toal, Graduate Student, [hidden email]
Brady Lab, UC Davis, Life Sciences 2243
One Shields Ave., Davis, CA  95616, ph: <a href="tel:%28530%29%20752-2537" value="+15307522537" target="_blank">(530) 752-2537







------------------------------------------------------------------------------
"Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
Instantly run your Selenium tests across 300+ browser/OS combos.  Get
unparalleled scalability from the best Selenium testing platform available.
Simple to use. Nothing to install. Get started now for free."
http://p.sf.net/sfu/SauceLabs
_______________________________________________
Gmod-ajax mailing list
[hidden email]
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

------------------------------------------------------------------------------
"Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
Instantly run your Selenium tests across 300+ browser/OS combos.  Get
unparalleled scalability from the best Selenium testing platform available.
Simple to use. Nothing to install. Get started now for free."
http://p.sf.net/sfu/SauceLabs
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Re: Install on OSX Mavericks

vkrishna
Hi Ted,

If you didn’t want to go through the process of standing up your own JBrowse, I would like to direct your attention to a resource called “CoGe” (a Comparative Genomics portal, developed, hosted and run by Eric Lyons group at the University of Arizona, accessible here: http://genomevolution.org/CoGe/).

They host a vast number of whole genomes (multiple assembly and/or annotation versions) plus supporting data. This resource is backed by the iPlant Cyberinfrastructure initiative. Recently they have updated their “GenomeView” component which allows users to visualize genomic data, from their proprietary viewer to JBrowse.

You can search through their huge list of organisms here: http://genomevolution.org/CoGe/OrganismView.pl. Once you have chosen the organism -> genome version -> dataset -> chromosome of your interest (in this case Solanum lycopersicum -> v2.40 -> chromosomes -> ch00), you can click on “Launch Genome Viewer” which takes to an GenomeView page, with an embedded JBrowse. This automatically loads the Gene Models track (based on the GFF from their database) by default. Here is the JBrowse for tomato: http://genomevolution.org/CoGe/GenomeView.pl?z=6&x=20000&gid=12289&chr=SL2.40ch00&loc=SL2.40ch01%3A1..287800&tracks=features&highlight=

If you want to add more tracks to this viewer, you can do so via a combination of the following methods:
  • As suggested by Scott in this thread, you can easily add BAM tracks from files stored on your desktop onto this instance using the JBrowse File > Open functionality. The limitation of this method is that there is no persistence of the data and it cannot be shared with other users.
  • Alternatively, CoGe offers user accounts (backed by the iPlant Datastore) which allows users to upload and store their data in the form of “Experiments” which can cataloged within “Notebooks”.
    • The user has the capability to make the uploaded data public, private or shared with a certain subset of CoGe users or a CoGe user group (for example you can make a group consisting of your lab members).
    • Once your data is on their system, you should be able to load an entire Notebook(s) and/or individual Experiment(s) to JBrowse as tracks.
    • Experiment(s) support quantitative tracks in csv,gtf,bed,gff formats, polymorphism in vcf format, alignments in bam format and sequence in fastq format.

They have extensive documentation on their CoGePedia about these tools and everything else they offer. http://genomevolution.org/wiki/index.php/Main_Page

Hope this is useful to you!

Incidentally, I am also in the process of trying to set up JBrowse on Mavericks (just got started). I will let you know in case I figure out a relatively straightforward method to get all the dependencies resolved.

Thank you.
Vivek

On Apr 30, 2014, at 8:15 PM, Scott Cain <[hidden email]> wrote:

Hi Ted,

Actually, that probably would work pretty well: you'd need to get the GFF for tomato from SGN and process it (which you would have had to do for your local install anyway), and once that processing is done, you could probably run the JBrowse server as a "micro" machine, which are free to run for the first year you have your account.  I don't think you could do the processing on a micro machine because they are pretty limited in CPU and memory.

For JBrowse, the size of the bam files doesn't matter, because you don't need to upload them if you're the only person using them: JBrowse will use the BAM files directly from your computer without uploading them (so it's pretty fast too).

Scott



On Wed, Apr 30, 2014 at 5:29 PM, Ted Toal <[hidden email]> wrote:
Thanks, Amelia.  But I want to be able to browse gigabytes of .bam files among other things.  That probably won't work.  I would also like to be able to install basically the entire Tomato genome on it with multiple tracks, plus some of our lab tracks.  Sol Genomics runs a gbrowse tomato browser with custom track support, but when I tried uploading it failed, and they told me they support only very small custom tracks.  Would the Cloud version support what I need?

ted

On Apr 30, 2014, at 2:18 PM, Amelia Ireland <[hidden email]> wrote:

Hi Ted,

You could try using GMOD in the Cloud, which is a virtual machine image in the Amazon Compute Cloud with JBrowse (plus other GMOD software) already set up on it. It takes very little time to get GMOD in the Cloud up and running, and you can run JBrowse on a "micro" instance because it's basically the browser that does all the work.

There is more information here:


This might be the quickest and easiest way to get JBrowse running if installing the dependencies on OS X is proving to be a nuisance.

Thanks,
Amelia.


On Wed, Apr 30, 2014 at 1:36 PM, Ted Toal <[hidden email]> wrote:
Yes, I have clicked on that link, and it does not work.  There are basic dependencies not yet installed.  I'm unable to install something called "expat", which seems to be a dependency of other required packages, and apparently this won't install because of a mixup somewhere in version numbers, with expat-2.1.0 getting mixed up with expat-2.0.1.  My frustration level is rising, it is beginning to feel like doing something on a Windows machine instead of a Mac.  I've spent way too much time on it.  I was hoping JBrowse would be a quick, easy, straightforward install that I could recommend to colleagues, and begin using it in my lab.  But I guess not.

ted

On Apr 30, 2014, at 12:42 PM, Deepak Unni <[hidden email]> wrote:

> Hi Ted,
>
> I also recently started using JBrowse.
> In my case, even after installing all the dependencies, I still saw that message.
>
> Have you tried clicking on 'Volvox test data here' link on the same page?
> I have attached an image highlighting the link.
>
> If JBrowse does load when you click this link then you should be all set.
>
> If not, then as Scott mentioned, you should look at setup.log for any errors.
>
> Best,
>
> Deepak
>
> On Wednesday, April 30, 2014 2:36 PM, Ted Toal <[hidden email]> wrote:
> Hello Amelia,
>
> Yes, I did get Apache up on and running on OS X Mavericks.  That part is working.
>
> ted
>
> On Apr 30, 2014, at 11:09 AM, Amelia Ireland <[hidden email]> wrote:
>
>> Hello Ted,
>>
>> Have you already got Apache up and running on OS X Mavericks successfully? IIRC, it isn't turned on automatically and you'll need to do a little configuration work first.
>>
>> Let us know what the situation is.
>>
>> Thanks,
>> Amelia.
>>
>>
>> On Wed, Apr 30, 2014 at 8:56 AM, Ted Toal <[hidden email]> wrote:
>> I'm trying to install JBrowse on my Macbook running OSX Mavericks.  The quick installation process seemed to complete ok, but when I try to access it I get the page with this error:
>>
>> However, JBrowse could not start, either because it has not yet been configured and loaded with data, or because of an error.
>>
>> The JBrowse Configuration Guide says to run ./setup.sh without sudo, but I ran it with sudo.  I suppose this messed things up.  I removed the entire JBrowse-1.11.3 folder and re-unzipped and re-ran ./setup.sh, but the same error occurs.
>>
>> I don't see any troubleshooting guide in the JBrowse Configuration Guide, nor any reference to a place to go that might describe troubleshooting.
>>
>> I'm wondering if there are prerequisites I'm missing.  I didn't do any prerequisites installation.  I already have XCode installed so I have a C compiler.  The JBrowse Config Guide says to do this on Ubuntu:
>>
>> sudo apt-get install zlib1g-dev libpng-dev libgd2-noxpm-dev build-essential
>>
>> But since I don't have Ubuntu, I'm hesitant to just try that.
>>
>> ttoal
>>
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
>> Instantly run your Selenium tests across 300+ browser/OS combos.  Get
>> unparalleled scalability from the best Selenium testing platform available.
>> Simple to use. Nothing to install. Get started now for free."
>> http://p.sf.net/sfu/SauceLabs
>> _______________________________________________
>> Gmod-ajax mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>>
>>
>> --
>> Amelia Ireland
>> GMOD Community Support
>> Generic Model Organism Database project
>> http://gmod.org || @gmodproject
>>
>
> --
> Ted Toal, Graduate Student, [hidden email]
> Brady Lab, UC Davis, Life Sciences 2243
> One Shields Ave., Davis, CA  95616, ph: <a href="tel:%28530%29%20752-2537" value="+15307522537" target="_blank">(530) 752-2537
>
>
>
>
>
>
>
> ------------------------------------------------------------------------------
> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
> Instantly run your Selenium tests across 300+ browser/OS combos.  Get
> unparalleled scalability from the best Selenium testing platform available.
> Simple to use. Nothing to install. Get started now for free."
> http://p.sf.net/sfu/SauceLabs
>
> _______________________________________________
> Gmod-ajax mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
>
> <JBrowse.png>

--
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Brady Lab, UC Davis, Life Sciences 2243
One Shields Ave., Davis, CA  95616, ph: <a href="tel:%28530%29%20752-2537" value="+15307522537" target="_blank">(530) 752-2537









--
Amelia Ireland
GMOD Community Support
Generic Model Organism Database project
http://gmod.org || @gmodproject


--
Ted Toal, Graduate Student, [hidden email]
Brady Lab, UC Davis, Life Sciences 2243
One Shields Ave., Davis, CA  95616, ph: <a href="tel:%28530%29%20752-2537" value="+15307522537" target="_blank">(530) 752-2537







------------------------------------------------------------------------------
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Instantly run your Selenium tests across 300+ browser/OS combos.  Get
unparalleled scalability from the best Selenium testing platform available.
Simple to use. Nothing to install. Get started now for free."
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------------------------------------------------------------------------
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GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research
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Re: Install on OSX Mavericks

Scott Cain
Hi Vivek,

Brilliant, I forgot the CoGe would likely have tomato data; that is likely a much better solution (unless he wants the fun of running his own browser :-)

Thanks,
Scott


Sent from my iPhone

On Apr 30, 2014, at 9:00 PM, "Krishnakumar, Vivek" <[hidden email]> wrote:

Hi Ted,

If you didn’t want to go through the process of standing up your own JBrowse, I would like to direct your attention to a resource called “CoGe” (a Comparative Genomics portal, developed, hosted and run by Eric Lyons group at the University of Arizona, accessible here: http://genomevolution.org/CoGe/).

They host a vast number of whole genomes (multiple assembly and/or annotation versions) plus supporting data. This resource is backed by the iPlant Cyberinfrastructure initiative. Recently they have updated their “GenomeView” component which allows users to visualize genomic data, from their proprietary viewer to JBrowse.

You can search through their huge list of organisms here: http://genomevolution.org/CoGe/OrganismView.pl. Once you have chosen the organism -> genome version -> dataset -> chromosome of your interest (in this case Solanum lycopersicum -> v2.40 -> chromosomes -> ch00), you can click on “Launch Genome Viewer” which takes to an GenomeView page, with an embedded JBrowse. This automatically loads the Gene Models track (based on the GFF from their database) by default. Here is the JBrowse for tomato: http://genomevolution.org/CoGe/GenomeView.pl?z=6&x=20000&gid=12289&chr=SL2.40ch00&loc=SL2.40ch01%3A1..287800&tracks=features&highlight=

If you want to add more tracks to this viewer, you can do so via a combination of the following methods:
  • As suggested by Scott in this thread, you can easily add BAM tracks from files stored on your desktop onto this instance using the JBrowse File > Open functionality. The limitation of this method is that there is no persistence of the data and it cannot be shared with other users.
  • Alternatively, CoGe offers user accounts (backed by the iPlant Datastore) which allows users to upload and store their data in the form of “Experiments” which can cataloged within “Notebooks”.
    • The user has the capability to make the uploaded data public, private or shared with a certain subset of CoGe users or a CoGe user group (for example you can make a group consisting of your lab members).
    • Once your data is on their system, you should be able to load an entire Notebook(s) and/or individual Experiment(s) to JBrowse as tracks.
    • Experiment(s) support quantitative tracks in csv,gtf,bed,gff formats, polymorphism in vcf format, alignments in bam format and sequence in fastq format.

They have extensive documentation on their CoGePedia about these tools and everything else they offer. http://genomevolution.org/wiki/index.php/Main_Page

Hope this is useful to you!

Incidentally, I am also in the process of trying to set up JBrowse on Mavericks (just got started). I will let you know in case I figure out a relatively straightforward method to get all the dependencies resolved.

Thank you.
Vivek

On Apr 30, 2014, at 8:15 PM, Scott Cain <[hidden email]> wrote:

Hi Ted,

Actually, that probably would work pretty well: you'd need to get the GFF for tomato from SGN and process it (which you would have had to do for your local install anyway), and once that processing is done, you could probably run the JBrowse server as a "micro" machine, which are free to run for the first year you have your account.  I don't think you could do the processing on a micro machine because they are pretty limited in CPU and memory.

For JBrowse, the size of the bam files doesn't matter, because you don't need to upload them if you're the only person using them: JBrowse will use the BAM files directly from your computer without uploading them (so it's pretty fast too).

Scott



On Wed, Apr 30, 2014 at 5:29 PM, Ted Toal <[hidden email]> wrote:
Thanks, Amelia.  But I want to be able to browse gigabytes of .bam files among other things.  That probably won't work.  I would also like to be able to install basically the entire Tomato genome on it with multiple tracks, plus some of our lab tracks.  Sol Genomics runs a gbrowse tomato browser with custom track support, but when I tried uploading it failed, and they told me they support only very small custom tracks.  Would the Cloud version support what I need?

ted

On Apr 30, 2014, at 2:18 PM, Amelia Ireland <[hidden email]> wrote:

Hi Ted,

You could try using GMOD in the Cloud, which is a virtual machine image in the Amazon Compute Cloud with JBrowse (plus other GMOD software) already set up on it. It takes very little time to get GMOD in the Cloud up and running, and you can run JBrowse on a "micro" instance because it's basically the browser that does all the work.

There is more information here:


This might be the quickest and easiest way to get JBrowse running if installing the dependencies on OS X is proving to be a nuisance.

Thanks,
Amelia.


On Wed, Apr 30, 2014 at 1:36 PM, Ted Toal <[hidden email]> wrote:
Yes, I have clicked on that link, and it does not work.  There are basic dependencies not yet installed.  I'm unable to install something called "expat", which seems to be a dependency of other required packages, and apparently this won't install because of a mixup somewhere in version numbers, with expat-2.1.0 getting mixed up with expat-2.0.1.  My frustration level is rising, it is beginning to feel like doing something on a Windows machine instead of a Mac.  I've spent way too much time on it.  I was hoping JBrowse would be a quick, easy, straightforward install that I could recommend to colleagues, and begin using it in my lab.  But I guess not.

ted

On Apr 30, 2014, at 12:42 PM, Deepak Unni <[hidden email]> wrote:

> Hi Ted,
>
> I also recently started using JBrowse.
> In my case, even after installing all the dependencies, I still saw that message.
>
> Have you tried clicking on 'Volvox test data here' link on the same page?
> I have attached an image highlighting the link.
>
> If JBrowse does load when you click this link then you should be all set.
>
> If not, then as Scott mentioned, you should look at setup.log for any errors.
>
> Best,
>
> Deepak
>
> On Wednesday, April 30, 2014 2:36 PM, Ted Toal <[hidden email]> wrote:
> Hello Amelia,
>
> Yes, I did get Apache up on and running on OS X Mavericks.  That part is working.
>
> ted
>
> On Apr 30, 2014, at 11:09 AM, Amelia Ireland <[hidden email]> wrote:
>
>> Hello Ted,
>>
>> Have you already got Apache up and running on OS X Mavericks successfully? IIRC, it isn't turned on automatically and you'll need to do a little configuration work first.
>>
>> Let us know what the situation is.
>>
>> Thanks,
>> Amelia.
>>
>>
>> On Wed, Apr 30, 2014 at 8:56 AM, Ted Toal <[hidden email]> wrote:
>> I'm trying to install JBrowse on my Macbook running OSX Mavericks.  The quick installation process seemed to complete ok, but when I try to access it I get the page with this error:
>>
>> However, JBrowse could not start, either because it has not yet been configured and loaded with data, or because of an error.
>>
>> The JBrowse Configuration Guide says to run ./setup.sh without sudo, but I ran it with sudo.  I suppose this messed things up.  I removed the entire JBrowse-1.11.3 folder and re-unzipped and re-ran ./setup.sh, but the same error occurs.
>>
>> I don't see any troubleshooting guide in the JBrowse Configuration Guide, nor any reference to a place to go that might describe troubleshooting.
>>
>> I'm wondering if there are prerequisites I'm missing.  I didn't do any prerequisites installation.  I already have XCode installed so I have a C compiler.  The JBrowse Config Guide says to do this on Ubuntu:
>>
>> sudo apt-get install zlib1g-dev libpng-dev libgd2-noxpm-dev build-essential
>>
>> But since I don't have Ubuntu, I'm hesitant to just try that.
>>
>> ttoal
>>
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
>> Instantly run your Selenium tests across 300+ browser/OS combos.  Get
>> unparalleled scalability from the best Selenium testing platform available.
>> Simple to use. Nothing to install. Get started now for free."
>> http://p.sf.net/sfu/SauceLabs
>> _______________________________________________
>> Gmod-ajax mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>>
>>
>> --
>> Amelia Ireland
>> GMOD Community Support
>> Generic Model Organism Database project
>> http://gmod.org || @gmodproject
>>
>
> --
> Ted Toal, Graduate Student, [hidden email]
> Brady Lab, UC Davis, Life Sciences 2243
> One Shields Ave., Davis, CA  95616, ph: <a href="tel:%28530%29%20752-2537" value="+15307522537" target="_blank">(530) 752-2537
>
>
>
>
>
>
>
> ------------------------------------------------------------------------------
> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
> Instantly run your Selenium tests across 300+ browser/OS combos.  Get
> unparalleled scalability from the best Selenium testing platform available.
> Simple to use. Nothing to install. Get started now for free."
> http://p.sf.net/sfu/SauceLabs
>
> _______________________________________________
> Gmod-ajax mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
>
> <JBrowse.png>

--
Ted Toal, Graduate Student, [hidden email]
Brady Lab, UC Davis, Life Sciences 2243
One Shields Ave., Davis, CA  95616, ph: <a href="tel:%28530%29%20752-2537" value="+15307522537" target="_blank">(530) 752-2537









--
Amelia Ireland
GMOD Community Support
Generic Model Organism Database project
http://gmod.org || @gmodproject


--
Ted Toal, Graduate Student, [hidden email]
Brady Lab, UC Davis, Life Sciences 2243
One Shields Ave., Davis, CA  95616, ph: <a href="tel:%28530%29%20752-2537" value="+15307522537" target="_blank">(530) 752-2537







------------------------------------------------------------------------------
"Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
Instantly run your Selenium tests across 300+ browser/OS combos.  Get
unparalleled scalability from the best Selenium testing platform available.
Simple to use. Nothing to install. Get started now for free."
http://p.sf.net/sfu/SauceLabs
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research
------------------------------------------------------------------------------
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Instantly run your Selenium tests across 300+ browser/OS combos.  Get
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Re: Install on OSX Mavericks

Keiran Raine
In reply to this post by Ted Toal
Hi Ted,

The easiest way to deal with things that struggle to install on a Mac these days is to use VirtualBox with a Linux image, say Ubuntu.

Then installing packages is through standard apt-get (or other package manager).

Once it's running you should be able to use your standard Mac browser and open the files in your native environment[1].  If you want them pre-configured you can use 'shared folders'[2] so the virtual device can see your local areas.

FYI, use nginx to serve the site on Linux it's far simpler to work with.

[1] I've not done this but technically it should work
[2] It's documented but milage may vary

Hope this helps,

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

Tel:+44 (0)1223 834244 Ext: 7703
Office: H104

On 30 Apr 2014, at 16:56, Ted Toal <[hidden email]> wrote:

I'm trying to install JBrowse on my Macbook running OSX Mavericks.  The quick installation process seemed to complete ok, but when I try to access it I get the page with this error:

However, JBrowse could not start, either because it has not yet been configured and loaded with data, or because of an error.

The JBrowse Configuration Guide says to run ./setup.sh without sudo, but I ran it with sudo.  I suppose this messed things up.  I removed the entire JBrowse-1.11.3 folder and re-unzipped and re-ran ./setup.sh, but the same error occurs.

I don't see any troubleshooting guide in the JBrowse Configuration Guide, nor any reference to a place to go that might describe troubleshooting.

I'm wondering if there are prerequisites I'm missing.  I didn't do any prerequisites installation.  I already have XCode installed so I have a C compiler.  The JBrowse Config Guide says to do this on Ubuntu:

sudo apt-get install zlib1g-dev libpng-dev libgd2-noxpm-dev build-essential

But since I don't have Ubuntu, I'm hesitant to just try that.

ttoal





------------------------------------------------------------------------------
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Instantly run your Selenium tests across 300+ browser/OS combos.  Get
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Re: Install on OSX Mavericks

Ted Toal
Thanks, Keiran.

I worry that I may be pushing my little MacBook too far by installing and running VirtualBox, running a virtual machine running Ubuntu Linux.  It is getting more complex than I wanted, and is telling me that JBrowse may not be suitable as a personal genome data browser on one's laptop, but is probably targeted more at running on a server and servicing many users?  

I'm going to have to check into the GMOD in the Cloud that Scott mentioned, that might be the best solution.  I'd really like to set up a lab browser that everybody in my lab could both use and add tracks to.  Our lab has no access to a server with a web server, except perhaps for free cloud services.

ted


On May 1, 2014, at 1:57 AM, Keiran Raine <[hidden email]> wrote:

Hi Ted,

The easiest way to deal with things that struggle to install on a Mac these days is to use VirtualBox with a Linux image, say Ubuntu.

Then installing packages is through standard apt-get (or other package manager).

Once it's running you should be able to use your standard Mac browser and open the files in your native environment[1].  If you want them pre-configured you can use 'shared folders'[2] so the virtual device can see your local areas.

FYI, use nginx to serve the site on Linux it's far simpler to work with.

[1] I've not done this but technically it should work
[2] It's documented but milage may vary

Hope this helps,

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

Tel:+44 (0)1223 834244 Ext: 7703
Office: H104

On 30 Apr 2014, at 16:56, Ted Toal <[hidden email]> wrote:

I'm trying to install JBrowse on my Macbook running OSX Mavericks.  The quick installation process seemed to complete ok, but when I try to access it I get the page with this error:

However, JBrowse could not start, either because it has not yet been configured and loaded with data, or because of an error.

The JBrowse Configuration Guide says to run ./setup.sh without sudo, but I ran it with sudo.  I suppose this messed things up.  I removed the entire JBrowse-1.11.3 folder and re-unzipped and re-ran ./setup.sh, but the same error occurs.

I don't see any troubleshooting guide in the JBrowse Configuration Guide, nor any reference to a place to go that might describe troubleshooting.

I'm wondering if there are prerequisites I'm missing.  I didn't do any prerequisites installation.  I already have XCode installed so I have a C compiler.  The JBrowse Config Guide says to do this on Ubuntu:

sudo apt-get install zlib1g-dev libpng-dev libgd2-noxpm-dev build-essential

But since I don't have Ubuntu, I'm hesitant to just try that.

ttoal





------------------------------------------------------------------------------
"Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
Instantly run your Selenium tests across 300+ browser/OS combos.  Get
unparalleled scalability from the best Selenium testing platform available.
Simple to use. Nothing to install. Get started now for free."
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-- The Wellcome Trust 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.

--
Ted Toal, Graduate Student, [hidden email]
Brady Lab, UC Davis, Life Sciences 2243
One Shields Ave., Davis, CA  95616, ph: (530) 752-2537







------------------------------------------------------------------------------
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Instantly run your Selenium tests across 300+ browser/OS combos.  Get
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Simple to use. Nothing to install. Get started now for free."
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Re: Install on OSX Mavericks

Raymond Wan

Hi Ted,


Quoting Ted Toal <[hidden email]>:

> I worry that I may be pushing my little MacBook too far by installing and
> running VirtualBox, running a virtual machine running Ubuntu Linux.  It is
> getting more complex than I wanted, and is telling me that JBrowse may not be
> suitable as a personal genome data browser on one's laptop, but is probably
> targeted more at running on a server and servicing many users?  


While running a virtual machine has its advantages, I have to admit that I'm not
a big fan of it since it's really like running two computers on a single machine
(i.e., the host and the virtual one) at the same time.  At least those of us
who've succeeded on Ubuntu can help you a bit better.

Sounds to me like your original problem was the installation of prerequisites
but all the other [good] options being given are changing the topic slightly.
If you are adamant about getting this working on an OSX, I guess by going back
and forth between the log files and Google, you'll succeed...some day.  :-)

JBrowse could be run one one's laptop but that assumes you're the only user
accessing it, of course.  I've ran JBrowse on a laptop and a desktop before
without any problems in terms of CPU power (though I might have been more
accepting of the slower response time).  However, I was running Ubuntu on
it...

Ray




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Re: Install on OSX Mavericks

Colin
I don't know the exact error that is the issue here, but there is a known problem with setup.sh when using the latest version of BioPerl when setting up the Yeast example data. This problem is due to a change in the latest BioPerl, but it will be fixed in the next version of JBrowse (coming soon!)

If you would like to try to fix it yourself (the exact error message in setup.log might say "MSG: No suitable files found in sample_data/raw/yeast_chr1+2" for future reference), then please run the following in the jbrowse directory
gunzip -c sample_data/raw/yeast_scaffolds/chr1.fa.gz sample_data/raw/yeast_scaffolds/chr2.fa.gzip > sample_data/raw/yeast_chr1+2/yeast.fa;

Then rerun setup.sh
Sorry for the trouble. Running on mac osx shouldn't normally be an issue, but if you experience further problems you let us know

Thanks
-Colin




On Thu, May 1, 2014 at 10:59 AM, Raymond Wan <[hidden email]> wrote:

Hi Ted,


Quoting Ted Toal <[hidden email]>:

> I worry that I may be pushing my little MacBook too far by installing and
> running VirtualBox, running a virtual machine running Ubuntu Linux.  It is
> getting more complex than I wanted, and is telling me that JBrowse may not be
> suitable as a personal genome data browser on one's laptop, but is probably
> targeted more at running on a server and servicing many users?


While running a virtual machine has its advantages, I have to admit that I'm not
a big fan of it since it's really like running two computers on a single machine
(i.e., the host and the virtual one) at the same time.  At least those of us
who've succeeded on Ubuntu can help you a bit better.

Sounds to me like your original problem was the installation of prerequisites
but all the other [good] options being given are changing the topic slightly.
If you are adamant about getting this working on an OSX, I guess by going back
and forth between the log files and Google, you'll succeed...some day.  :-)

JBrowse could be run one one's laptop but that assumes you're the only user
accessing it, of course.  I've ran JBrowse on a laptop and a desktop before
without any problems in terms of CPU power (though I might have been more
accepting of the slower response time).  However, I was running Ubuntu on
it...

Ray




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Re: Install on OSX Mavericks

Colin
Sorry I didn't see the issue with dependencies. My last post would not fix this problem with those.

-Colin


On Sun, May 4, 2014 at 11:20 AM, Colin <[hidden email]> wrote:
I don't know the exact error that is the issue here, but there is a known problem with setup.sh when using the latest version of BioPerl when setting up the Yeast example data. This problem is due to a change in the latest BioPerl, but it will be fixed in the next version of JBrowse (coming soon!)

If you would like to try to fix it yourself (the exact error message in setup.log might say "MSG: No suitable files found in sample_data/raw/yeast_chr1+2" for future reference), then please run the following in the jbrowse directory
gunzip -c sample_data/raw/yeast_scaffolds/chr1.fa.gz sample_data/raw/yeast_scaffolds/chr2.fa.gzip > sample_data/raw/yeast_chr1+2/yeast.fa;

Then rerun setup.sh
Sorry for the trouble. Running on mac osx shouldn't normally be an issue, but if you experience further problems you let us know

Thanks
-Colin




On Thu, May 1, 2014 at 10:59 AM, Raymond Wan <[hidden email]> wrote:

Hi Ted,


Quoting Ted Toal <[hidden email]>:

> I worry that I may be pushing my little MacBook too far by installing and
> running VirtualBox, running a virtual machine running Ubuntu Linux.  It is
> getting more complex than I wanted, and is telling me that JBrowse may not be
> suitable as a personal genome data browser on one's laptop, but is probably
> targeted more at running on a server and servicing many users?


While running a virtual machine has its advantages, I have to admit that I'm not
a big fan of it since it's really like running two computers on a single machine
(i.e., the host and the virtual one) at the same time.  At least those of us
who've succeeded on Ubuntu can help you a bit better.

Sounds to me like your original problem was the installation of prerequisites
but all the other [good] options being given are changing the topic slightly.
If you are adamant about getting this working on an OSX, I guess by going back
and forth between the log files and Google, you'll succeed...some day.  :-)

JBrowse could be run one one's laptop but that assumes you're the only user
accessing it, of course.  I've ran JBrowse on a laptop and a desktop before
without any problems in terms of CPU power (though I might have been more
accepting of the slower response time).  However, I was running Ubuntu on
it...

Ray




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Simple to use. Nothing to install. Get started now for free."
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Re: Install on OSX Mavericks

Colin
Hi all,

Sorry my last post was off-topic.

I wanted to see if I could help out with using fink, so I created a fresh install with it, then I just used "fink install libpng16". After this, I had to set the include and linker paths manually since fink installs to a different directory that is not normally picked up.

export CXXFLAGS=-I/sw/include/
export LDFLAGS=-L/sw/lib/
./setup.sh

Then the setup.sh script completed without error. I agree that it would be great to document these steps somewhere in more detail, but I hope this helps for now! 

-Colin

PS keep an eye out for a new jbrowse release soon. It will support high resolution screens and it looks great on retina displays :)




On Sun, May 4, 2014 at 11:50 AM, Colin <[hidden email]> wrote:
Sorry I didn't see the issue with dependencies. My last post would not fix this problem with those.

-Colin


On Sun, May 4, 2014 at 11:20 AM, Colin <[hidden email]> wrote:
I don't know the exact error that is the issue here, but there is a known problem with setup.sh when using the latest version of BioPerl when setting up the Yeast example data. This problem is due to a change in the latest BioPerl, but it will be fixed in the next version of JBrowse (coming soon!)

If you would like to try to fix it yourself (the exact error message in setup.log might say "MSG: No suitable files found in sample_data/raw/yeast_chr1+2" for future reference), then please run the following in the jbrowse directory
gunzip -c sample_data/raw/yeast_scaffolds/chr1.fa.gz sample_data/raw/yeast_scaffolds/chr2.fa.gzip > sample_data/raw/yeast_chr1+2/yeast.fa;

Then rerun setup.sh
Sorry for the trouble. Running on mac osx shouldn't normally be an issue, but if you experience further problems you let us know

Thanks
-Colin




On Thu, May 1, 2014 at 10:59 AM, Raymond Wan <[hidden email]> wrote:

Hi Ted,


Quoting Ted Toal <[hidden email]>:

> I worry that I may be pushing my little MacBook too far by installing and
> running VirtualBox, running a virtual machine running Ubuntu Linux.  It is
> getting more complex than I wanted, and is telling me that JBrowse may not be
> suitable as a personal genome data browser on one's laptop, but is probably
> targeted more at running on a server and servicing many users?


While running a virtual machine has its advantages, I have to admit that I'm not
a big fan of it since it's really like running two computers on a single machine
(i.e., the host and the virtual one) at the same time.  At least those of us
who've succeeded on Ubuntu can help you a bit better.

Sounds to me like your original problem was the installation of prerequisites
but all the other [good] options being given are changing the topic slightly.
If you are adamant about getting this working on an OSX, I guess by going back
and forth between the log files and Google, you'll succeed...some day.  :-)

JBrowse could be run one one's laptop but that assumes you're the only user
accessing it, of course.  I've ran JBrowse on a laptop and a desktop before
without any problems in terms of CPU power (though I might have been more
accepting of the slower response time).  However, I was running Ubuntu on
it...

Ray




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------------------------------------------------------------------------------
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Instantly run your Selenium tests across 300+ browser/OS combos.  Get
unparalleled scalability from the best Selenium testing platform available.
Simple to use. Nothing to install. Get started now for free."
http://p.sf.net/sfu/SauceLabs
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