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  1. IGB
  2. IGBF-1479

Identify genome versions without HEADER.md files

        Details

        • Type: Story
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
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          Description

          Review all genome version directories in IGB Quickload. Identify directories where there is no HEADER.md available. Make note of any genomes that are lacking a HEADER.md in the comments here.

          See: https://svn.bioviz.org/viewvc for easy way to browse the directories. Alternatively, could write a bash script to check them all at once. Describe process used here.

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              Task - A task that needs to be done. IGBF-2582 Add HEADER.md to quickload directories

              • Major - Major loss of function.
              • Closed

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                Jill Jill Jenkins (Inactive) added a comment - - edited

                On a Mac:

                find . -type d '!' -exec test -e "{}/HEADER.md" ';' -print | sort

                ./A_thaliana_Apr_2008
                ./A_thaliana_Jun_2009
                ./B_distachyon_Aug_2010
                ./C_albicans_SC5314_Jun_2014
                ./C_albicans_SC5314_Nov_2008
                ./C_albicans_WO-1_Dec_2013
                ./C_albicans_WO-1_Jul_2010
                ./C_papaya_Aug_2010
                ./C_reinhardtii_Nov_2010
                ./F_vesca_Sep_2011
                ./G_max_Aug_2010
                ./H_sapiens_Dec_2013/UCSCTracks
                ./M_truncatula_Mar_2009
                ./O_sativa_japonica_Jun_2009
                ./P_persica_Apr_2010
                ./P_trichocarpa_Jan_2010
                ./R_communis_May_2008
                ./S_bicolor_Jan_2009
                ./S_pombe_May_2012
                ./S_tuberosum_DM_Jul_2011
                ./T_castaneum_Mar_2008
                ./T_kodakaraensis_KOD1_May_2004
                ./V_carteri_Jul_2010
                ./Z_mays_B73_Mar_2010

                Show
                Jill Jill Jenkins (Inactive) added a comment - - edited On a Mac: find . -type d '!' -exec test -e "{}/HEADER.md" ';' -print | sort ./A_thaliana_Apr_2008 ./A_thaliana_Jun_2009 ./B_distachyon_Aug_2010 ./C_albicans_SC5314_Jun_2014 ./C_albicans_SC5314_Nov_2008 ./C_albicans_WO-1_Dec_2013 ./C_albicans_WO-1_Jul_2010 ./C_papaya_Aug_2010 ./C_reinhardtii_Nov_2010 ./F_vesca_Sep_2011 ./G_max_Aug_2010 ./H_sapiens_Dec_2013/UCSCTracks ./M_truncatula_Mar_2009 ./O_sativa_japonica_Jun_2009 ./P_persica_Apr_2010 ./P_trichocarpa_Jan_2010 ./R_communis_May_2008 ./S_bicolor_Jan_2009 ./S_pombe_May_2012 ./S_tuberosum_DM_Jul_2011 ./T_castaneum_Mar_2008 ./T_kodakaraensis_KOD1_May_2004 ./V_carteri_Jul_2010 ./Z_mays_B73_Mar_2010
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                inaylor Irvin Naylor (Inactive) added a comment -

                Command: find ./quickload -type d '!' -exec test -e "{}/HEADER.md" ';' -print | sort
                Ran in directory integrated-genome-browser/core

                ./quickload
                ./quickload/src
                ./quickload/src/main
                ./quickload/src/main/java
                ./quickload/src/main/java/org
                ./quickload/src/main/java/org/lorainelab
                ./quickload/src/main/java/org/lorainelab/igb
                ./quickload/src/main/java/org/lorainelab/igb/quickload
                ./quickload/src/main/java/org/lorainelab/igb/quickload/model
                ./quickload/src/main/java/org/lorainelab/igb/quickload/model/annots
                ./quickload/src/main/java/org/lorainelab/igb/quickload/util
                ./quickload/src/main/resources
                ./quickload/src/test
                ./quickload/src/test/java
                ./quickload/src/test/java/org
                ./quickload/src/test/java/org/lorainelab
                ./quickload/src/test/java/org/lorainelab/igb
                ./quickload/src/test/java/org/lorainelab/igb/quickload
                ./quickload/src/test/java/org/lorainelab/igb/quickload/utils
                ./quickload/src/test/resources
                ./quickload/src/test/resources/A_thaliana_Jun_2009
                ./quickload/src/test/resources/quickload
                ./quickload/src/test/resources/quickload/A_thaliana_Jun_2009
                ./quickload/src/test/resources/quickload/H_sapiens_Dec_2013

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                inaylor Irvin Naylor (Inactive) added a comment - Command: find ./quickload -type d '!' -exec test -e "{}/HEADER.md" ';' -print | sort Ran in directory integrated-genome-browser/core ./quickload ./quickload/src ./quickload/src/main ./quickload/src/main/java ./quickload/src/main/java/org ./quickload/src/main/java/org/lorainelab ./quickload/src/main/java/org/lorainelab/igb ./quickload/src/main/java/org/lorainelab/igb/quickload ./quickload/src/main/java/org/lorainelab/igb/quickload/model ./quickload/src/main/java/org/lorainelab/igb/quickload/model/annots ./quickload/src/main/java/org/lorainelab/igb/quickload/util ./quickload/src/main/resources ./quickload/src/test ./quickload/src/test/java ./quickload/src/test/java/org ./quickload/src/test/java/org/lorainelab ./quickload/src/test/java/org/lorainelab/igb ./quickload/src/test/java/org/lorainelab/igb/quickload ./quickload/src/test/java/org/lorainelab/igb/quickload/utils ./quickload/src/test/resources ./quickload/src/test/resources/A_thaliana_Jun_2009 ./quickload/src/test/resources/quickload ./quickload/src/test/resources/quickload/A_thaliana_Jun_2009 ./quickload/src/test/resources/quickload/H_sapiens_Dec_2013
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                ann.loraine Ann Loraine added a comment -

                Sorry, the description was not clear enough.
                By "quickload," I meant the site that we use to distribute data to IGB, not the quickload module in the IGB bitbucket repository.
                However I just now checked a few of the directories Jill listed in her comment and it looks like her output is correct.
                The next step will be to add the header files. Making a new issue for that.

                Show
                ann.loraine Ann Loraine added a comment - Sorry, the description was not clear enough. By "quickload," I meant the site that we use to distribute data to IGB, not the quickload module in the IGB bitbucket repository. However I just now checked a few of the directories Jill listed in her comment and it looks like her output is correct. The next step will be to add the header files. Making a new issue for that.

                  People

                  • Assignee:
                    inaylor Irvin Naylor (Inactive)
                    Reporter:
                    ann.loraine Ann Loraine
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                      Updated:
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