Information regarding setting up GBrowse for Research

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Information regarding setting up GBrowse for Research

Sai Susheel Sunkara

Hi,

I am Susheel from Southern Illinois University Carbondale from USA. I belong to research computing team of Information Technology department here in the university. We have our genomics team here working on soybean genome and trying to upload their findings and results to online. So we as a part of IT team are requested for setting up the GBrowse for the concerned team. Since we started working on it we are finding hard time in proceeding with the GBrowse installation and configuring. Therefore while I was browsing online regarding help, I encountered with your email id. I would like to know if your concerned or any of the team , can setup a GBrowse genome browser for us  from scratch and provide us with readily usable platform where our research team can upload their findings?


Regards
Sai Susheel


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Re: Information regarding setting up GBrowse for Research

Scott Cain
Hi Susheel,

GBrowse is getting fairly old and most new projects that are setting up genome browsers with GMOD components are choosing to do so with JBrowse (http://jbrowse.org/).  Is there a reason your group does not want to do that?  It is generally much easier to set up.

If you do want to stick with GBrowse, I can also tell you that it is much easier to set up GBrowse on some systems than others.  For example, on Debian-based systems like Ubuntu, you can use apt-get to either get all of the prerequisites for GBrowse and then install GBrowse itself by hand (which is what I tend to do) or even install GBrowse via apt-get as well.  On systems that use yum it is also possible to get most (possibly all) prerequisites via yum but I am less familiar with the state of development of those systems.

Another option if you wanted to use Amazon AWS, I can suggest GMOD in the Cloud, which is an AWS image that has GBrowse preinstalled on it.  The image itself is a few years old, but there hasn't been much development in GBrowse since then so it should be pretty much usable out of the box.

Finally, as you are moving along, you can certainly ask on this mailing list for help with specific problems.  We're generally pretty good about answering.

Scott


On Wed, Apr 12, 2017 at 11:18 AM, Sai Susheel Sunkara <[hidden email]> wrote:

Hi,

I am Susheel from Southern Illinois University Carbondale from USA. I belong to research computing team of Information Technology department here in the university. We have our genomics team here working on soybean genome and trying to upload their findings and results to online. So we as a part of IT team are requested for setting up the GBrowse for the concerned team. Since we started working on it we are finding hard time in proceeding with the GBrowse installation and configuring. Therefore while I was browsing online regarding help, I encountered with your email id. I would like to know if your concerned or any of the team , can setup a GBrowse genome browser for us  from scratch and provide us with readily usable platform where our research team can upload their findings?


Regards
Sai Susheel


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GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: Information regarding setting up GBrowse for Research

Sai Susheel Sunkara

Hey Scott,

Thank you for the information. We are indeed working on jbrowse too parallely, where we are equally facing certain issues in feeding the input and seeing the results. However that may not be purely a concerned issue for you guys(since not related to installation). regarding to option of installing gbrowse on ubuntu, I tried that too, however, I could not move forward after the complete installation as per the guides from online, i.e., facing issue to actually launch gbrowse. 

So, going forward while trying it again, can I pose questions about it here on this list?(regarding configuring gbrowse)

Regards
Sai Susheel


From: Scott Cain <[hidden email]>
Sent: Wednesday, April 12, 2017 1:11:21 PM
To: Sai Susheel Sunkara
Cc: [hidden email]
Subject: Re: [Gmod-gbrowse] Information regarding setting up GBrowse for Research
 
Hi Susheel,

GBrowse is getting fairly old and most new projects that are setting up genome browsers with GMOD components are choosing to do so with JBrowse (http://jbrowse.org/).  Is there a reason your group does not want to do that?  It is generally much easier to set up.

If you do want to stick with GBrowse, I can also tell you that it is much easier to set up GBrowse on some systems than others.  For example, on Debian-based systems like Ubuntu, you can use apt-get to either get all of the prerequisites for GBrowse and then install GBrowse itself by hand (which is what I tend to do) or even install GBrowse via apt-get as well.  On systems that use yum it is also possible to get most (possibly all) prerequisites via yum but I am less familiar with the state of development of those systems.

Another option if you wanted to use Amazon AWS, I can suggest GMOD in the Cloud, which is an AWS image that has GBrowse preinstalled on it.  The image itself is a few years old, but there hasn't been much development in GBrowse since then so it should be pretty much usable out of the box.

Finally, as you are moving along, you can certainly ask on this mailing list for help with specific problems.  We're generally pretty good about answering.

Scott


On Wed, Apr 12, 2017 at 11:18 AM, Sai Susheel Sunkara <[hidden email]> wrote:

Hi,

I am Susheel from Southern Illinois University Carbondale from USA. I belong to research computing team of Information Technology department here in the university. We have our genomics team here working on soybean genome and trying to upload their findings and results to online. So we as a part of IT team are requested for setting up the GBrowse for the concerned team. Since we started working on it we are finding hard time in proceeding with the GBrowse installation and configuring. Therefore while I was browsing online regarding help, I encountered with your email id. I would like to know if your concerned or any of the team , can setup a GBrowse genome browser for us  from scratch and provide us with readily usable platform where our research team can upload their findings?


Regards
Sai Susheel


------------------------------------------------------------------------------
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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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Re: Information regarding setting up GBrowse for Research

Scott Cain
Yes, definitely ask questions on the list! :-)

Scott


On Wed, Apr 12, 2017 at 2:21 PM, Sai Susheel Sunkara <[hidden email]> wrote:

Hey Scott,

Thank you for the information. We are indeed working on jbrowse too parallely, where we are equally facing certain issues in feeding the input and seeing the results. However that may not be purely a concerned issue for you guys(since not related to installation). regarding to option of installing gbrowse on ubuntu, I tried that too, however, I could not move forward after the complete installation as per the guides from online, i.e., facing issue to actually launch gbrowse. 

So, going forward while trying it again, can I pose questions about it here on this list?(regarding configuring gbrowse)

Regards
Sai Susheel


From: Scott Cain <[hidden email]>
Sent: Wednesday, April 12, 2017 1:11:21 PM
To: Sai Susheel Sunkara
Cc: [hidden email]
Subject: Re: [Gmod-gbrowse] Information regarding setting up GBrowse for Research
 
Hi Susheel,

GBrowse is getting fairly old and most new projects that are setting up genome browsers with GMOD components are choosing to do so with JBrowse (http://jbrowse.org/).  Is there a reason your group does not want to do that?  It is generally much easier to set up.

If you do want to stick with GBrowse, I can also tell you that it is much easier to set up GBrowse on some systems than others.  For example, on Debian-based systems like Ubuntu, you can use apt-get to either get all of the prerequisites for GBrowse and then install GBrowse itself by hand (which is what I tend to do) or even install GBrowse via apt-get as well.  On systems that use yum it is also possible to get most (possibly all) prerequisites via yum but I am less familiar with the state of development of those systems.

Another option if you wanted to use Amazon AWS, I can suggest GMOD in the Cloud, which is an AWS image that has GBrowse preinstalled on it.  The image itself is a few years old, but there hasn't been much development in GBrowse since then so it should be pretty much usable out of the box.

Finally, as you are moving along, you can certainly ask on this mailing list for help with specific problems.  We're generally pretty good about answering.

Scott


On Wed, Apr 12, 2017 at 11:18 AM, Sai Susheel Sunkara <[hidden email]> wrote:

Hi,

I am Susheel from Southern Illinois University Carbondale from USA. I belong to research computing team of Information Technology department here in the university. We have our genomics team here working on soybean genome and trying to upload their findings and results to online. So we as a part of IT team are requested for setting up the GBrowse for the concerned team. Since we started working on it we are finding hard time in proceeding with the GBrowse installation and configuring. Therefore while I was browsing online regarding help, I encountered with your email id. I would like to know if your concerned or any of the team , can setup a GBrowse genome browser for us  from scratch and provide us with readily usable platform where our research team can upload their findings?


Regards
Sai Susheel


------------------------------------------------------------------------------
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engaging tech sites, Slashdot.org! http://sdm.link/slashdot
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:(216)%20392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research

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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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Re: Information regarding setting up GBrowse for Research

Fields, Christopher J

Just chiming in from a bit further up the state of Illinois…

 

I agree with Scott.  We’ve had a few requests for doing essentially what you are being tasked with, and we have been moving away from GBrowse (not actively developed) to JBrowse (actively maintained).  The AWS GMOD in the Cloud is a good place to start (and I’m guessing updates to the latest JBrowse should be available?)

 

Just curious, but would this be a long-term resource?  A key issue we had in the past (and address up-front now) is long-term maintenance of these and similar app deployments.  Initial deployment and setup is the most time consuming step, but there is a long-term (at least partial) time commitment to maintain everything.   For instance, a web-based genome browser is a common request with assembly projects, but downstream after deployment you will likely have requests coming in on updates to the assembly (or assemblies), addition of new data, hardware and web server maintenance, etc., which is something researchers don’t necessarily think about when budgeting.

 

chris

 

From: Scott Cain <[hidden email]>
Date: Wednesday, April 12, 2017 at 1:47 PM
To: Sai Susheel Sunkara <[hidden email]>
Cc: GMOD-Gbrowse <[hidden email]>
Subject: Re: [Gmod-gbrowse] Information regarding setting up GBrowse for Research

 

Yes, definitely ask questions on the list! :-)

 

Scott

 

 

On Wed, Apr 12, 2017 at 2:21 PM, Sai Susheel Sunkara <[hidden email]> wrote:

Hey Scott,

Thank you for the information. We are indeed working on jbrowse too parallely, where we are equally facing certain issues in feeding the input and seeing the results. However that may not be purely a concerned issue for you guys(since not related to installation). regarding to option of installing gbrowse on ubuntu, I tried that too, however, I could not move forward after the complete installation as per the guides from online, i.e., facing issue to actually launch gbrowse. 

So, going forward while trying it again, can I pose questions about it here on this list?(regarding configuring gbrowse)

Regards
Sai Susheel


From: Scott Cain <[hidden email]>
Sent: Wednesday, April 12, 2017 1:11:21 PM
To: Sai Susheel Sunkara
Cc: [hidden email]
Subject: Re: [Gmod-gbrowse] Information regarding setting up GBrowse for Research

 

Hi Susheel,

 

GBrowse is getting fairly old and most new projects that are setting up genome browsers with GMOD components are choosing to do so with JBrowse (http://jbrowse.org/).  Is there a reason your group does not want to do that?  It is generally much easier to set up.

 

If you do want to stick with GBrowse, I can also tell you that it is much easier to set up GBrowse on some systems than others.  For example, on Debian-based systems like Ubuntu, you can use apt-get to either get all of the prerequisites for GBrowse and then install GBrowse itself by hand (which is what I tend to do) or even install GBrowse via apt-get as well.  On systems that use yum it is also possible to get most (possibly all) prerequisites via yum but I am less familiar with the state of development of those systems.

 

Another option if you wanted to use Amazon AWS, I can suggest GMOD in the Cloud, which is an AWS image that has GBrowse preinstalled on it.  The image itself is a few years old, but there hasn't been much development in GBrowse since then so it should be pretty much usable out of the box.

 

Finally, as you are moving along, you can certainly ask on this mailing list for help with specific problems.  We're generally pretty good about answering.

 

Scott

 

 

On Wed, Apr 12, 2017 at 11:18 AM, Sai Susheel Sunkara <[hidden email]> wrote:

Hi,

I am Susheel from Southern Illinois University Carbondale from USA. I belong to research computing team of Information Technology department here in the university. We have our genomics team here working on soybean genome and trying to upload their findings and results to online. So we as a part of IT team are requested for setting up the GBrowse for the concerned team. Since we started working on it we are finding hard time in proceeding with the GBrowse installation and configuring. Therefore while I was browsing online regarding help, I encountered with your email id. I would like to know if your concerned or any of the team , can setup a GBrowse genome browser for us  from scratch and provide us with readily usable platform where our research team can upload their findings?


Regards

Sai Susheel


------------------------------------------------------------------------------
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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[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse



 

--

------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:(216)%20392-3087" target="_blank">216-392-3087
Ontario Institute for Cancer Research


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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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Re: Information regarding setting up GBrowse for Research

Sai Susheel Sunkara

Not sure if it is long term project. I cannot comment upon that.
Thanks for the help.
I will reach out to you guys  if I face issues with jbrowse as currently we stopped checking with gbrowse.


From: Fields, Christopher J <[hidden email]>
Sent: Wednesday, April 12, 2017 2:13:42 PM
To: Scott Cain; Sai Susheel Sunkara
Cc: [hidden email]
Subject: Re: [Gmod-gbrowse] Information regarding setting up GBrowse for Research
 

Just chiming in from a bit further up the state of Illinois…

 

I agree with Scott.  We’ve had a few requests for doing essentially what you are being tasked with, and we have been moving away from GBrowse (not actively developed) to JBrowse (actively maintained).  The AWS GMOD in the Cloud is a good place to start (and I’m guessing updates to the latest JBrowse should be available?)

 

Just curious, but would this be a long-term resource?  A key issue we had in the past (and address up-front now) is long-term maintenance of these and similar app deployments.  Initial deployment and setup is the most time consuming step, but there is a long-term (at least partial) time commitment to maintain everything.   For instance, a web-based genome browser is a common request with assembly projects, but downstream after deployment you will likely have requests coming in on updates to the assembly (or assemblies), addition of new data, hardware and web server maintenance, etc., which is something researchers don’t necessarily think about when budgeting.

 

chris

 

From: Scott Cain <[hidden email]>
Date: Wednesday, April 12, 2017 at 1:47 PM
To: Sai Susheel Sunkara <[hidden email]>
Cc: GMOD-Gbrowse <[hidden email]>
Subject: Re: [Gmod-gbrowse] Information regarding setting up GBrowse for Research

 

Yes, definitely ask questions on the list! :-)

 

Scott

 

 

On Wed, Apr 12, 2017 at 2:21 PM, Sai Susheel Sunkara <[hidden email]> wrote:

Hey Scott,

Thank you for the information. We are indeed working on jbrowse too parallely, where we are equally facing certain issues in feeding the input and seeing the results. However that may not be purely a concerned issue for you guys(since not related to installation). regarding to option of installing gbrowse on ubuntu, I tried that too, however, I could not move forward after the complete installation as per the guides from online, i.e., facing issue to actually launch gbrowse. 

So, going forward while trying it again, can I pose questions about it here on this list?(regarding configuring gbrowse)

Regards
Sai Susheel


From: Scott Cain <[hidden email]>
Sent: Wednesday, April 12, 2017 1:11:21 PM
To: Sai Susheel Sunkara
Cc: [hidden email]
Subject: Re: [Gmod-gbrowse] Information regarding setting up GBrowse for Research

 

Hi Susheel,

 

GBrowse is getting fairly old and most new projects that are setting up genome browsers with GMOD components are choosing to do so with JBrowse (http://jbrowse.org/).  Is there a reason your group does not want to do that?  It is generally much easier to set up.

 

If you do want to stick with GBrowse, I can also tell you that it is much easier to set up GBrowse on some systems than others.  For example, on Debian-based systems like Ubuntu, you can use apt-get to either get all of the prerequisites for GBrowse and then install GBrowse itself by hand (which is what I tend to do) or even install GBrowse via apt-get as well.  On systems that use yum it is also possible to get most (possibly all) prerequisites via yum but I am less familiar with the state of development of those systems.

 

Another option if you wanted to use Amazon AWS, I can suggest GMOD in the Cloud, which is an AWS image that has GBrowse preinstalled on it.  The image itself is a few years old, but there hasn't been much development in GBrowse since then so it should be pretty much usable out of the box.

 

Finally, as you are moving along, you can certainly ask on this mailing list for help with specific problems.  We're generally pretty good about answering.

 

Scott

 

 

On Wed, Apr 12, 2017 at 11:18 AM, Sai Susheel Sunkara <[hidden email]> wrote:

Hi,

I am Susheel from Southern Illinois University Carbondale from USA. I belong to research computing team of Information Technology department here in the university. We have our genomics team here working on soybean genome and trying to upload their findings and results to online. So we as a part of IT team are requested for setting up the GBrowse for the concerned team. Since we started working on it we are finding hard time in proceeding with the GBrowse installation and configuring. Therefore while I was browsing online regarding help, I encountered with your email id. I would like to know if your concerned or any of the team , can setup a GBrowse genome browser for us  from scratch and provide us with readily usable platform where our research team can upload their findings?


Regards

Sai Susheel


------------------------------------------------------------------------------
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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--

------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:(216)%20392-3087" target="_blank">216-392-3087
Ontario Institute for Cancer Research


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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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