Bowtie2 and tophat2 data library set up

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Bowtie2 and tophat2 data library set up

huayan
Hi,

I wanted to use bowtie2 and tophat2 locally. I remembered you have instructions about how to set up the library here, but it is not accessible any more.
https://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup

Can you direct me to the right page or send me the documents please?

Thanks,
Huayan

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Re: Bowtie2 and tophat2 data library set up

Martin Čech
Hello Huayan,

I don't know why the wiki page disappeared and I will investigate it. In the meantime I have found a cached copy for you: http://webcache.googleusercontent.com/search?q=cache:SWWpt6XsmCkJ:https://wiki.galaxyproject.org/Admin/NGS%2520Local%2520Setup+&cd=1&hl=en&ct=clnk&gl=us

Martin, Galaxy team


On Wed, Mar 19, 2014 at 9:44 PM, Huayan Gao <[hidden email]> wrote:
Hi,

I wanted to use bowtie2 and tophat2 locally. I remembered you have instructions about how to set up the library here, but it is not accessible any more.
https://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup

Can you direct me to the right page or send me the documents please?

Thanks,
Huayan

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

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  http://galaxyproject.org/search/mailinglists/


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Re: Bowtie2 and tophat2 data library set up

Martin Čech
Hello again Huayan,

the page got renamed and redirect was not in place. I have put it there and the new page has even more info on it! :)

thank you for using Galaxy!

Martin


On Wed, Mar 19, 2014 at 10:18 PM, Martin Čech <[hidden email]> wrote:
Hello Huayan,

I don't know why the wiki page disappeared and I will investigate it. In the meantime I have found a cached copy for you: http://webcache.googleusercontent.com/search?q=cache:SWWpt6XsmCkJ:https://wiki.galaxyproject.org/Admin/NGS%2520Local%2520Setup+&cd=1&hl=en&ct=clnk&gl=us

Martin, Galaxy team


On Wed, Mar 19, 2014 at 9:44 PM, Huayan Gao <[hidden email]> wrote:
Hi,

I wanted to use bowtie2 and tophat2 locally. I remembered you have instructions about how to set up the library here, but it is not accessible any more.
https://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup

Can you direct me to the right page or send me the documents please?

Thanks,
Huayan

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/



___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

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Re: Bowtie2 and tophat2 data library set up

huayan
Thanks Martin!

One more question, I want to install all the migrated tools from stage 9, that is NGS tools to my local galaxy. I tried but always got some problems.
Do you have the instructions on wiki too?

Thanks,
Huayan


On Thu, Mar 20, 2014 at 10:27 AM, Martin Čech <[hidden email]> wrote:
Hello again Huayan,

the page got renamed and redirect was not in place. I have put it there and the new page has even more info on it! :)

thank you for using Galaxy!

Martin


On Wed, Mar 19, 2014 at 10:18 PM, Martin Čech <[hidden email]> wrote:
Hello Huayan,

I don't know why the wiki page disappeared and I will investigate it. In the meantime I have found a cached copy for you: http://webcache.googleusercontent.com/search?q=cache:SWWpt6XsmCkJ:https://wiki.galaxyproject.org/Admin/NGS%2520Local%2520Setup+&cd=1&hl=en&ct=clnk&gl=us

Martin, Galaxy team


On Wed, Mar 19, 2014 at 9:44 PM, Huayan Gao <[hidden email]> wrote:
Hi,

I wanted to use bowtie2 and tophat2 locally. I remembered you have instructions about how to set up the library here, but it is not accessible any more.
https://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup

Can you direct me to the right page or send me the documents please?

Thanks,
Huayan

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/




___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
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Re: Bowtie2 and tophat2 data library set up

huayan
Hi Martin,

Actually I want a "NGS Toolbox Beta" tool panel exactly like the usegalaxy.org. How can I achieve this?
I found myself looking for the tools and put them to tool_conf.xml which is very tedious.
Is there a better way to do it?


Best,
Huayan


On Thu, Mar 20, 2014 at 11:43 AM, Huayan Gao <[hidden email]> wrote:
Thanks Martin!

One more question, I want to install all the migrated tools from stage 9, that is NGS tools to my local galaxy. I tried but always got some problems.
Do you have the instructions on wiki too?

Thanks,
Huayan


On Thu, Mar 20, 2014 at 10:27 AM, Martin Čech <[hidden email]> wrote:
Hello again Huayan,

the page got renamed and redirect was not in place. I have put it there and the new page has even more info on it! :)

thank you for using Galaxy!

Martin


On Wed, Mar 19, 2014 at 10:18 PM, Martin Čech <[hidden email]> wrote:
Hello Huayan,

I don't know why the wiki page disappeared and I will investigate it. In the meantime I have found a cached copy for you: http://webcache.googleusercontent.com/search?q=cache:SWWpt6XsmCkJ:https://wiki.galaxyproject.org/Admin/NGS%2520Local%2520Setup+&cd=1&hl=en&ct=clnk&gl=us

Martin, Galaxy team


On Wed, Mar 19, 2014 at 9:44 PM, Huayan Gao <[hidden email]> wrote:
Hi,

I wanted to use bowtie2 and tophat2 locally. I remembered you have instructions about how to set up the library here, but it is not accessible any more.
https://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup

Can you direct me to the right page or send me the documents please?

Thanks,
Huayan

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/





___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
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Re: Bowtie2 and tophat2 data library set up

Martin Čech
Hi Huayan,

these tools should mostly be available from the Tool Shed (Galaxy's appstore). You can install them easily into any Galaxy that you are an admin of. Please see more information here: https://wiki.galaxyproject.org/Admin/Tools

Martin,
galaxy team


On Thu, Mar 20, 2014 at 1:57 AM, Huayan Gao <[hidden email]> wrote:
Hi Martin,

Actually I want a "NGS Toolbox Beta" tool panel exactly like the usegalaxy.org. How can I achieve this?
I found myself looking for the tools and put them to tool_conf.xml which is very tedious.
Is there a better way to do it?


Best,
Huayan


On Thu, Mar 20, 2014 at 11:43 AM, Huayan Gao <[hidden email]> wrote:
Thanks Martin!

One more question, I want to install all the migrated tools from stage 9, that is NGS tools to my local galaxy. I tried but always got some problems.
Do you have the instructions on wiki too?

Thanks,
Huayan


On Thu, Mar 20, 2014 at 10:27 AM, Martin Čech <[hidden email]> wrote:
Hello again Huayan,

the page got renamed and redirect was not in place. I have put it there and the new page has even more info on it! :)

thank you for using Galaxy!

Martin


On Wed, Mar 19, 2014 at 10:18 PM, Martin Čech <[hidden email]> wrote:
Hello Huayan,

I don't know why the wiki page disappeared and I will investigate it. In the meantime I have found a cached copy for you: http://webcache.googleusercontent.com/search?q=cache:SWWpt6XsmCkJ:https://wiki.galaxyproject.org/Admin/NGS%2520Local%2520Setup+&cd=1&hl=en&ct=clnk&gl=us

Martin, Galaxy team


On Wed, Mar 19, 2014 at 9:44 PM, Huayan Gao <[hidden email]> wrote:
Hi,

I wanted to use bowtie2 and tophat2 locally. I remembered you have instructions about how to set up the library here, but it is not accessible any more.
https://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup

Can you direct me to the right page or send me the documents please?

Thanks,
Huayan

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/






___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/