Uploaded image for project: 'IGB'
  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
    • Labels:

      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.

        Attachments

          Issue Links

            Activity

            Hide
            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
            Hide
            inaylor Irvin Naylor 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

            Show
            inaylor Irvin Naylor 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
            Hide
            aloraine 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
            aloraine 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
                Reporter:
                aloraine Ann Loraine
              • Votes:
                0 Vote for this issue
                Watchers:
                3 Start watching this issue

                Dates

                • Created:
                  Updated:
                  Resolved: