question on galaxy reference genome window
Dear Galaxy members, I am new to galaxy and just installed galaxy on aws cloud. I am testing how it works and have the following question below: 1. I tried to test bowtie2 with the dataset I uploaded, however, the window for reference genome is very narrow and nothing from pull-down menu can be selected. When I omit that option to execute bowtie2, galaxy give error message for requesting reference genome. I am using hg19, should I upload myself? If so, how? 2. Same error happen for me to run fastqc --- the reference genome selection window is way too narrow and nothing can be selected Thank you very much for your inputs and helps! Kind regards, Kathryn
Kathryn, Are you using the galaxy cloud configuration provided by the team, or have you installed your own galaxy on a cloud instance? It sounds like the latter, in which case you'll need to configure reference as detailed here: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup. You may also want to experiment with using the preconfigured cloud instances, see this page for more information on those: http://wiki.galaxyproject.org/CloudMan -Dannon On Dec 18, 2012, at 2:21 PM, "Sun, Wenping [USA]" <Sun_Wenping@bah.com> wrote:
Dear Galaxy members,
I am new to galaxy and just installed galaxy on aws cloud. I am testing how it works and have the following question below:
1. I tried to test bowtie2 with the dataset I uploaded, however, the window for reference genome is very narrow and nothing from pull-down menu can be selected. When I omit that option to execute bowtie2, galaxy give error message for requesting reference genome. I am using hg19, should I upload myself? If so, how? 2. Same error happen for me to run fastqc --- the reference genome selection window is way too narrow and nothing can be selected
Thank you very much for your inputs and helps! Kind regards, Kathryn
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
Hi Dannon, Yes, you are correct! I installed galaxy from scratch on the cloud. I will check the site you provided and see how it goes. I also have the preconfigured cloud instance set up recently. However, when I stopped the instances (master and cluster nodes) from aws, I couldn't get the galaxy web running again (the instance running however the DNS not able to access). What is the right steps to stop the instances and restart it next time? Thank you in advance, Kathryn -----Original Message----- From: Dannon Baker [mailto:dannonbaker@me.com] Sent: Wednesday, December 19, 2012 10:27 AM To: Sun, Wenping [USA] Cc: galaxy-user@bx.psu.edu Subject: [External] Re: [galaxy-user] question on galaxy reference genome window Kathryn, Are you using the galaxy cloud configuration provided by the team, or have you installed your own galaxy on a cloud instance? It sounds like the latter, in which case you'll need to configure reference as detailed here: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup. You may also want to experiment with using the preconfigured cloud instances, see this page for more information on those: http://wiki.galaxyproject.org/CloudMan -Dannon On Dec 18, 2012, at 2:21 PM, "Sun, Wenping [USA]" <Sun_Wenping@bah.com> wrote:
Dear Galaxy members,
I am new to galaxy and just installed galaxy on aws cloud. I am testing how it works and have the following question below:
1. I tried to test bowtie2 with the dataset I uploaded, however, the window for reference genome is very narrow and nothing from pull-down menu can be selected. When I omit that option to execute bowtie2, galaxy give error message for requesting reference genome. I am using hg19, should I upload myself? If so, how? 2. Same error happen for me to run fastqc --- the reference genome selection window is way too narrow and nothing can be selected
Thank you very much for your inputs and helps! Kind regards, Kathryn
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
On Dec 19, 2012, at 11:09 AM, "Sun, Wenping [USA]" <Sun_Wenping@bah.com> wrote:
I also have the preconfigured cloud instance set up recently. However, when I stopped the instances (master and cluster nodes) from aws, I couldn't get the galaxy web running again (the instance running however the DNS not able to access). What is the right steps to stop the instances and restart it next time?
The cloud deployment isn't designed to be stopped/started through the AWS console -- that'll definitely cause problems. Instead, just terminate the instance through the cloudman interface and when you want to use the cluster again simply use the same clustername and start a new instance. The old data will be automatically mounted (the cluster details are saved in S3 and the data is all on an EBS volume that's persisted in your account) and you'll be right back where you left off.
participants (2)
-
Dannon Baker -
Sun, Wenping [USA]