Re: [galaxy-user] [galaxy-dev] Create and Transfer Galaxy Page
Hi Todd,
[Not sure if this is better suited to galaxy-dev or -user, so I'm sending to both].
galaxy-user is most appropriate for this question because it related to usage of Galaxy; galaxy-dev is for local installation and tool development questions.
My question is - can I create a Galaxy 'Published Page' from my local Galaxy instance/histories, and then transfer that page to the main Galaxy instance?
Not currently, though this is in our long-term plan.
The reason is that I cannot make my local Galaxy instance public, as I am using a campus resource to host our galaxy. If this is possible, how can I do that? If not, any other ideas?
It is possible to move datasets and workflows relatively easily between instances, so I'd recommend that: (a) you move your data and workflows to our public instance; (b) rerun your analyses on the public instance to create the required; (c) create and host the Page on our public instance. You can be assured that we will maintain our public server over the coming years and your Page will remain available and have a stable URL.
Also, are there any tutorials/pages on how to create Published Pages in Galaxy in the first place?
Not yet, though the idea is for the Page editor to be self explanatory. Here's how to get started with Pages: (a) from User menu, go to Saved Pages; (b) create a Page; (c) edit the Page using the Web-based editor; there are menus for inserting embedded datasets, workflows, histories, and visualizations as well as performing standard word-processing operations. Let us know if you have problems/questions and we'll start a guide for creating Pages. Best, J.
Galaxy What is the best method in Galaxy to compare a Illumina data set to a 1500 bp known sequence? Scott Scott Tighe Advanced Genome Technology Lab Vermont Cancer Center at the University of Vermont 149 Beaumont Avenue Health Science Research Bd RM 305 Burlington Vermont USA 05405 lab 802-656-AGTC (2482) cell 802-999-6666
Hi Scott, If your Illumina data is DNA, then using either Bowtie (no indels) or BWA (supports indels) with the known sequence as a 'custom reference genome' would be a good choice. If RNA, then doing the same, but using TopHat instead, would be recommended. To use your known sequences as a custom reference genome, first load it in fasta format as a dataset into your history. Then at run time set the mapping tool form options to use a reference genome 'from the history'. There's no criteria around the actual content of a reference genome (can be a single short sequence), but the format should be standard fasta. http://wiki.g2.bx.psu.edu/Support#Custom_reference_genome Please let us know if you need more assistance, Best, Jen Galaxy team On 4/18/12 4:15 AM, Scott Tighe wrote:
Galaxy
What is the best method in Galaxy to compare a Illumina data set to a 1500 bp known sequence?
Scott
Scott Tighe Advanced Genome Technology Lab Vermont Cancer Center at the University of Vermont 149 Beaumont Avenue Health Science Research Bd RM 305 Burlington Vermont USA 05405 lab 802-656-AGTC (2482) cell 802-999-6666
___________________________________________________________ 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:
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Jeremy - Thanks so much for your helpful responses. One problem that i didn't mention with implementing your suggestions is that the histories I want to post contain mainly new tools that my lab developed for phylogenetics using transcriptome data. Therefore, the public instance does not have most of the tools in the history (we will put these on the tool shed as soon as we can). In addition, the analyses are VERY computationally intensive, including assembly and Maximum Likelihood analyses, and therefore probably are not suitable for re-running on the public Galaxy instance. (This is also a reason why I cannot make my local galaxy instance public - it exposes too many tools that could bog down the host computer). Additional suggestions most welcome… Todd On Apr 17, 2012, at 6:33 PM, Jeremy Goecks wrote:
Hi Todd,
[Not sure if this is better suited to galaxy-dev or -user, so I'm sending to both].
galaxy-user is most appropriate for this question because it related to usage of Galaxy; galaxy-dev is for local installation and tool development questions.
My question is - can I create a Galaxy 'Published Page' from my local Galaxy instance/histories, and then transfer that page to the main Galaxy instance?
Not currently, though this is in our long-term plan.
The reason is that I cannot make my local Galaxy instance public, as I am using a campus resource to host our galaxy. If this is possible, how can I do that? If not, any other ideas?
It is possible to move datasets and workflows relatively easily between instances, so I'd recommend that:
(a) you move your data and workflows to our public instance; (b) rerun your analyses on the public instance to create the required; (c) create and host the Page on our public instance.
You can be assured that we will maintain our public server over the coming years and your Page will remain available and have a stable URL.
Also, are there any tutorials/pages on how to create Published Pages in Galaxy in the first place?
Not yet, though the idea is for the Page editor to be self explanatory. Here's how to get started with Pages:
(a) from User menu, go to Saved Pages; (b) create a Page; (c) edit the Page using the Web-based editor; there are menus for inserting embedded datasets, workflows, histories, and visualizations as well as performing standard word-processing operations.
Let us know if you have problems/questions and we'll start a guide for creating Pages.
Best, J.
___________________________________________________________ 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:
Todd, There's not an ideal solution for your situation. My suggestion: (a) set up a cloud instance with your tools + a Page and use the "share-an-instance" feature so that others can access your data, tools, histories, and page in a single place ( http://wiki.g2.bx.psu.edu/Admin/Cloud ); (b) put your tools into the tool shed for easy access ( http://toolshed.g2.bx.psu.edu/ ); (c) replicate the page + as many of the histories as possible on our public server, with a note about how to get going with either (i) tools from the tool shed or (ii) on the cloud. We're working to make public server-cloud access more easy, so there may be something on the horizon that could smooth (c)(ii) out. Best, J. On Apr 18, 2012, at 5:02 PM, Todd Oakley wrote:
Jeremy - Thanks so much for your helpful responses.
One problem that i didn't mention with implementing your suggestions is that the histories I want to post contain mainly new tools that my lab developed for phylogenetics using transcriptome data. Therefore, the public instance does not have most of the tools in the history (we will put these on the tool shed as soon as we can). In addition, the analyses are VERY computationally intensive, including assembly and Maximum Likelihood analyses, and therefore probably are not suitable for re-running on the public Galaxy instance. (This is also a reason why I cannot make my local galaxy instance public - it exposes too many tools that could bog down the host computer).
Additional suggestions most welcome…
Todd
On Apr 17, 2012, at 6:33 PM, Jeremy Goecks wrote:
Hi Todd,
[Not sure if this is better suited to galaxy-dev or -user, so I'm sending to both].
galaxy-user is most appropriate for this question because it related to usage of Galaxy; galaxy-dev is for local installation and tool development questions.
My question is - can I create a Galaxy 'Published Page' from my local Galaxy instance/histories, and then transfer that page to the main Galaxy instance?
Not currently, though this is in our long-term plan.
The reason is that I cannot make my local Galaxy instance public, as I am using a campus resource to host our galaxy. If this is possible, how can I do that? If not, any other ideas?
It is possible to move datasets and workflows relatively easily between instances, so I'd recommend that:
(a) you move your data and workflows to our public instance; (b) rerun your analyses on the public instance to create the required; (c) create and host the Page on our public instance.
You can be assured that we will maintain our public server over the coming years and your Page will remain available and have a stable URL.
Also, are there any tutorials/pages on how to create Published Pages in Galaxy in the first place?
Not yet, though the idea is for the Page editor to be self explanatory. Here's how to get started with Pages:
(a) from User menu, go to Saved Pages; (b) create a Page; (c) edit the Page using the Web-based editor; there are menus for inserting embedded datasets, workflows, histories, and visualizations as well as performing standard word-processing operations.
Let us know if you have problems/questions and we'll start a guide for creating Pages.
Best, J.
___________________________________________________________ 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:
participants (4)
-
Jennifer Jackson -
Jeremy Goecks -
Scott Tighe -
Todd Oakley