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  1. IGB
  2. IGBF-1423

Add potato genome assembly synonyms to IGB species.txt

        Details

        • Story Points:
          0.25
        • Sprint:
          Fall 2018 Sprint 3

          Description

          Modify species.txt in IGB codebase

          Add line from:

          http://igbquickload.org/quickload/species.txt

          Preserve alphabetical order in file.

            Attachments

              Issue Links

              relates to

              Bug - A problem which impairs or prevents the functions of the product. HELP-276 Potato genome and transcriptome

              • To-Do

              Improvement - An improvement or enhancement to an existing feature or task. IGBF-1420 Add open access potato image to IGB start screen

              • Major - Major loss of function.
              • Closed

              Improvement - An improvement or enhancement to an existing feature or task. IGBF-1421 Add potato genome to IGB Quickload

              • Major - Major loss of function.
              • Closed

                Activity

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                ann.loraine Ann Loraine created issue -
                ann.loraine Ann Loraine made changes -
                Field Original Value New Value
                Link This issue relates to HELP-276 [ HELP-276 ]
                ann.loraine Ann Loraine made changes -
                Link This issue relates to IGBF-1420 [ IGBF-1420 ]
                ann.loraine Ann Loraine made changes -
                Link This issue relates to IGBF-1421 [ IGBF-1421 ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]
                ann.loraine Ann Loraine made changes -
                Description Add (or check to see if it is already there) the 4.04 DM potato genome to IGB synonyms.txt and species.txt files.

                IGB name for the assembly is:

                S_tuberosum_DM_Jan_2016

                To my knowledge, no other genome browser system is supporting this assembly, so there are no synonyms at the moment.

                For the name of the species, see the corresponding line in "contents.txt" in contents.txt genome assembly listing. See https://svn.bioviz.org/viewvc

                (Feel free to ask Dr. Loraine if you have questions.)                 		Add (or check to see if it is already there) the 4.03 DM potato genome to IGB synonyms.txt and species.txt files.

                To my knowledge, no other genome browser system is supporting this assembly, so there are no synonyms at the moment.

                For the name of the species, see the corresponding line in "contents.txt" in contents.txt genome assembly listing. See https://svn.bioviz.org/viewvc

                (Feel free to ask Dr. Loraine if you have questions.)
                ann.loraine Ann Loraine made changes -
                Description Add (or check to see if it is already there) the 4.03 DM potato genome to IGB synonyms.txt and species.txt files.

                To my knowledge, no other genome browser system is supporting this assembly, so there are no synonyms at the moment.

                For the name of the species, see the corresponding line in "contents.txt" in contents.txt genome assembly listing. See https://svn.bioviz.org/viewvc

                (Feel free to ask Dr. Loraine if you have questions.)                 		Modify species.txt in IGB codebase

                Add line from:

                http://igbquickload.org/quickload/species.txt

                Preserve alphabetical order in file.
                ann.loraine Ann Loraine made changes -
                Labels Beginner Intermediate
                ann.loraine Ann Loraine made changes -
                Comment [ Correction:

                *Only* modify species.txt

                Add line from:

                http://igbquickload.org/quickload/species.txt

                Preserve alphabetical order in file.

                Also, note we are now supporting the July 2011 version 4.03 release and not the version 4.04 Jan 2016 release. ]
                ann.loraine Ann Loraine made changes -
                Summary Add potato genome assembly synonyms to IGB species.txt and synonyms.txt Add potato genome assembly synonyms to IGB species.txt
                ann.loraine Ann Loraine made changes -
                Status Open [ 1 ] In Progress [ 3 ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Rank Ranked lower
                ann.loraine Ann Loraine made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
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                ann.loraine Ann Loraine added a comment - - edited

                Fixed on branch https://bitbucket.org/aloraine/alorainefork/branch/IGBF-1423

                To test:

                • Reset preferences to defaults
                • De-activate main IGB Quickload (which contains species.txt file listing potato; IGB uses species.txt files from Quickload sites in addition to its own personal species.txt file packaged with the installer)
                • Add this test Quickload site: http://lorainelab-quickload.scidas.org/IGBF-1423
                • Quit then re-start IGB
                • Check that the species and genome menus list the potato genome, with tooltip on mouse-over the species menu entry

                Note: To re-create this site in current working directory:

                svn (subversion) lets you check out part of a repository. This is the potato genome directory.

                Show
                ann.loraine Ann Loraine added a comment - - edited Fixed on branch https://bitbucket.org/aloraine/alorainefork/branch/IGBF-1423 To test: Reset preferences to defaults De-activate main IGB Quickload (which contains species.txt file listing potato; IGB uses species.txt files from Quickload sites in addition to its own personal species.txt file packaged with the installer) Add this test Quickload site: http://lorainelab-quickload.scidas.org/IGBF-1423 Quit then re-start IGB Check that the species and genome menus list the potato genome, with tooltip on mouse-over the species menu entry Note : To re-create this site in current working directory: svn co https://svn.bioviz.org/repos/genomes/quickload/S_tuberosum_DM_Jul_2011 wget -O - http://igbquickload.org/quickload/contents.txt | grep S_tuberosum_DM_Jul_2011 > contents.txt svn (subversion) lets you check out part of a repository. This is the potato genome directory.
                ann.loraine Ann Loraine made changes -
                Status Needs 1st Level Review [ 10005 ] Ready for Pull Request [ 10304 ]
                ann.loraine Ann Loraine made changes -
                Status Ready for Pull Request [ 10304 ] Needs 1st Level Review [ 10005 ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]
                ann.loraine Ann Loraine made changes -
                Status Needs 1st Level Review [ 10005 ] Reviewing [ 10301 ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]
                Hide
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                ann.loraine Ann Loraine added a comment -

                Passes functional review.

                Show
                ann.loraine Ann Loraine added a comment - Passes functional review.
                ann.loraine Ann Loraine made changes -
                Status Reviewing [ 10301 ] Ready for Pull Request [ 10304 ]
                ann.loraine Ann Loraine made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
                ann.loraine Ann Loraine made changes -
                Status Pull Request Submitted [ 10101 ] Needs Testing [ 10002 ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]
                Hide
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                ann.loraine Ann Loraine added a comment -

                Merged into upstream master (git@bitbucket.org:lorainelab/integrated-genome-browser.git)

                Show
                ann.loraine Ann Loraine added a comment - Merged into upstream master (git@bitbucket.org:lorainelab/integrated-genome-browser.git)
                ann.loraine Ann Loraine made changes -
                Resolution Done [ 10000 ]
                Status Needs Testing [ 10002 ] Closed [ 6 ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]
                ann.loraine Ann Loraine made changes -
                Workflow Loraine Lab Workflow [ 18129 ] Fall 2019 Workflow Update [ 19955 ]
                ann.loraine Ann Loraine made changes -
                Workflow Fall 2019 Workflow Update [ 19955 ] Revised Fall 2019 Workflow Update [ 22076 ]

                  People

                  • Assignee:
                    ann.loraine Ann Loraine
                    Reporter:
                    ann.loraine Ann Loraine
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                    Dates

                    • Created:
                      Updated:
                      Resolved: