Posting Supplementary Information On Galaxy Server

Question: Posting Supplementary Information On Galaxy Server

5.3 years ago by

Hello, I would like to know whether I can post my supplementary data for an article in the galaxy server. I have .docx files and .xlsx files. I am planning to upload these data in a folder and share the link at first and later publish it. When I tried uploading xlsx file, it is getting automatically converted to .xml files. Please let me know if it is possible provide the supplementary information through galaxy that includes doc and excel sheets.. Thank you so much for your help Jainy

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modified 5.3 years ago by Jennifer Hillman Jackson ♦ 25k • written 5.3 years ago by Jainy Tharun • 10

5.3 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hi Jainy, Currently .doc and .xlsx file formats are not supported on Pages directly. For .doc text and .xlsx graphic, you can copy/export as text and adjust format using the tools in Pages or upload it as a text dataset and link it in, or for graphics export the image and include it that way in the Page (a side effect of this is that items like graphs will be more immediately visible to your readers). And for .xlsx data, you might consider exporting and making that accessible in standard tabular (or interval, bed, etc.) format as a dataset instead, and linking that to the Page. This would permit your readers to work with the raw or computed data directly. There are also various compute tools, including custom (look under "Text Manipulation"), that could be created to make algorithms you set up in excel available to your readers directly as reusable tools in Galaxy (that could then be included in workflows, etc. to reproduce the methods). Galaxy also has graphing tools, which would accept datasets as inputs in a similar way that excel would, but these you have perhaps already seen. We realize that this can mean reorganizing data, potentially a significant portion, and it is likely not appropriate for every case - but I wanted to make known the current options. There is in general usually a way to do most data manipulation functions within Galaxy - finding the right combination of tools is the key. But, the appropriateness and value long-term of converting can vary of course. Should you need help with a specific case, please let us know and we can offer support. We think Pages are a great resource for communications, and we want to make it as easy as possible for folks to use them for publications. Examples can be found in the Published Pages section, with the "Using Galaxy" supplemental, protocol 2, demonstrating how to quickly convert even a seemingly foreign data file format into an interval format suitable for use with many tools. Hopefully this offers some useful alternatives! Jen Galaxy team -- Jennifer Hillman-Jackson http://galaxyproject.org

ADD COMMENT • link written 5.3 years ago by Jennifer Hillman Jackson ♦ 25k

Jennifer, We are also interested in using PSU galaxy to host a history for out supplemental methods. Based on your response, it looks like PSU is willing to support that use case. However, I'd like to know how long we can count on that link being available. Searching the wiki for "publish" or "supplement" I couldn't find anything that outlined the policy. As that would include the fastq files, the size would not trivial, and the account used may never be accessed again to run new jobs, until the next paper. How long will an *accessible* history be kept on the server? How long will a *published* history be kept on the server? How long will a published *page* ? Thank you very much! Regards, Curtis Are the rules different if it is made into "Pages"? To: Jainy Tharun Cc: galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] posting supplementary information on galaxy server Hi Jainy, Currently .doc and .xlsx file formats are not supported on Pages directly. For .doc text and .xlsx graphic, you can copy/export as text and adjust format using the tools in Pages or upload it as a text dataset and link it in, or for graphics export the image and include it that way in the Page (a side effect of this is that items like graphs will be more immediately visible to your readers). And for .xlsx data, you might consider exporting and making that accessible in standard tabular (or interval, bed, etc.) format as a dataset instead, and linking that to the Page. This would permit your readers to work with the raw or computed data directly. There are also various compute tools, including custom (look under "Text Manipulation"), that could be created to make algorithms you set up in excel available to your readers directly as reusable tools in Galaxy (that could then be included in workflows, etc. to reproduce the methods). Galaxy also has graphing tools, which would accept datasets as inputs in a similar way that excel would, but these you have perhaps already seen. We realize that this can mean reorganizing data, potentially a significant portion, and it is likely not appropriate for every case - but I wanted to make known the current options. There is in general usually a way to do most data manipulation functions within Galaxy - finding the right combination of tools is the key. But, the appropriateness and value long-term of converting can vary of course. Should you need help with a specific case, please let us know and we can offer support. We think Pages are a great resource for communications, and we want to make it as easy as possible for folks to use them for publications. Examples can be found in the Published Pages section, with the "Using Galaxy" supplemental, protocol 2, demonstrating how to quickly convert even a seemingly foreign data file format into an interval format suitable for use with many tools. Hopefully this offers some useful alternatives! Jen Galaxy team -- Jennifer Hillman-Jackson http://galaxyproject.org ___________________________________________________________ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/

ADD REPLY • link written 5.1 years ago by Robert Curtis Hendrickson • 130

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