Re: [galaxy-dev] Bowtie2 and tophat2 data library set up
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 huayan...@gmail.com 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 huayan...@gmail.com 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 mar...@bx.psu.edu 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 mar...@bx.psu.edu 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=1hl=enct=clnkgl=us Martin, Galaxy team On Wed, Mar 19, 2014 at 9:44 PM, Huayan Gao huayan...@gmail.comwrote: 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/
[galaxy-dev] Bowtie2 and tophat2 data library set up
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/
Re: [galaxy-dev] Bowtie2 and tophat2 data library set up
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=1hl=enct=clnkgl=us Martin, Galaxy team On Wed, Mar 19, 2014 at 9:44 PM, Huayan Gao huayan...@gmail.com 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/
Re: [galaxy-dev] Bowtie2 and tophat2 data library set up
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 mar...@bx.psu.edu 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=1hl=enct=clnkgl=us Martin, Galaxy team On Wed, Mar 19, 2014 at 9:44 PM, Huayan Gao huayan...@gmail.com 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/
Re: [galaxy-dev] Bowtie2 and tophat2 data library set up
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 mar...@bx.psu.edu 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 mar...@bx.psu.edu 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=1hl=enct=clnkgl=us Martin, Galaxy team On Wed, Mar 19, 2014 at 9:44 PM, Huayan Gao huayan...@gmail.com 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/
Re: [galaxy-dev] Bowtie2 and tophat2 data library set up
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 huayan...@gmail.com 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 mar...@bx.psu.edu 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 mar...@bx.psu.edu 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=1hl=enct=clnkgl=us Martin, Galaxy team On Wed, Mar 19, 2014 at 9:44 PM, Huayan Gao huayan...@gmail.com 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/
