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  1. IGB
  2. IGBF-3325

Copy KP 2023 data (30-804059537) to IGB Quickload host for visualization in IGB

        Details

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

          Description

          Kelsey's Palanivelu Lab

          Directory: /nobackup/tomato_genome/30-804059537-KP (kp for "Kelsey Pryze")

            Attachments

              Issue Links

              relates to

              Epic - Created by JIRA Software - do not edit or delete. Issue type for a big user story that needs to be broken down. IGBF-3251 Process and deploy Palanivelu Lab data

              • Major - Major loss of function.
              • To-Do

              Task - A task that needs to be done. IGBF-3324 Generate junction files Kelsey's Palanivelu Lab 2023

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-3328 Add KP 2023 multiqc report and sample CSV file to bitbucket

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-3323 Generate scaled coverage graphs Kelsey's Palanivelu Lab 2023

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-3326 Create KP 2023 sample sheet needed for Quickload site and more

              • Major - Major loss of function.
              • Closed

                Activity

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                Mdavis4290 Molly Davis created issue -
                Mdavis4290 Molly Davis made changes -
                Field Original Value New Value
                Epic Link IGBF-3251 [ 22132 ]
                Mdavis4290 Molly Davis made changes -
                Link This issue blocks IGBF-3323 [ IGBF-3323 ]
                Mdavis4290 Molly Davis made changes -
                Link This issue blocks IGBF-3324 [ IGBF-3324 ]
                Mdavis4290 Molly Davis made changes -
                Link This issue is blocked by IGBF-3326 [ IGBF-3326 ]
                Mdavis4290 Molly Davis made changes -
                Link This issue blocks IGBF-3323 [ IGBF-3323 ]
                Mdavis4290 Molly Davis made changes -
                Link This issue relates to IGBF-3323 [ IGBF-3323 ]
                Mdavis4290 Molly Davis made changes -
                Link This issue blocks IGBF-3324 [ IGBF-3324 ]
                Mdavis4290 Molly Davis made changes -
                Link This issue is blocked by IGBF-3326 [ IGBF-3326 ]
                Mdavis4290 Molly Davis made changes -
                Link This issue relates to IGBF-3324 [ IGBF-3324 ]
                Mdavis4290 Molly Davis made changes -
                Link This issue relates to IGBF-3251 [ IGBF-3251 ]
                Mdavis4290 Molly Davis made changes -
                Link This issue relates to IGBF-3328 [ IGBF-3328 ]
                Mdavis4290 Molly Davis made changes -
                Link This issue relates to IGBF-3326 [ IGBF-3326 ]
                ann.loraine Ann Loraine made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
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                ann.loraine Ann Loraine added a comment -

                I did not have write permission in the required subdirectories so I am putting copies of files to transfer in: /nobackup/tomato_genome/30-804059537-KP.results

                The RENCI host has about 555 Gb of space left. I'm not sure this will be enough.

                Show
                ann.loraine Ann Loraine added a comment - I did not have write permission in the required subdirectories so I am putting copies of files to transfer in: /nobackup/tomato_genome/30-804059537-KP.results The RENCI host has about 555 Gb of space left. I'm not sure this will be enough.
                Hide
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                ann.loraine Ann Loraine added a comment -

                The number of files to copy: 382
                The total size of files to copy: 147 Gb

                There is enough room on the host to accommodate the data.

                Show
                ann.loraine Ann Loraine added a comment - The number of files to copy: 382 The total size of files to copy: 147 Gb There is enough room on the host to accommodate the data.
                Hide
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                ann.loraine Ann Loraine added a comment - - edited

                Copying with:

                scp -J aloraine@hop.renci.org -r 30-804059537-KP.results aloraine@lorainelab-quickload.scidas.org:/projects/igbquickload/lorainelab/www/main/htdocs/hotpollen/S_lycopersicum_Jun_2022/pistil/.
                Show
                ann.loraine Ann Loraine added a comment - - edited Copying with: scp -J aloraine@hop.renci.org -r 30-804059537-KP.results aloraine@lorainelab-quickload.scidas.org:/projects/igbquickload/lorainelab/www/main/htdocs/hotpollen/S_lycopersicum_Jun_2022/pistil/.
                Hide
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                ann.loraine Ann Loraine added a comment -

                Files copied:

                [aloraine@lorainelab-quickload pistil]$ du -h
187G	.
[aloraine@lorainelab-quickload pistil]$ ls | wc -l
382
                Show
                ann.loraine Ann Loraine added a comment - Files copied: [aloraine@lorainelab-quickload pistil]$ du -h 187G . [aloraine@lorainelab-quickload pistil]$ ls | wc -l 382
                Hide
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                ann.loraine Ann Loraine added a comment -

                Files browsable at:

                http://lorainelab-quickload.scidas.org/hotpollen/S_lycopersicum_Jun_2022/pistil/

                Show
                ann.loraine Ann Loraine added a comment - Files browsable at: http://lorainelab-quickload.scidas.org/hotpollen/S_lycopersicum_Jun_2022/pistil/
                ann.loraine Ann Loraine made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                ann.loraine Ann Loraine made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                ann.loraine Ann Loraine made changes -
                Status First Level Review in Progress [ 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 ] Reviewing Pull Request [ 10303 ]
                ann.loraine Ann Loraine made changes -
                Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
                ann.loraine Ann Loraine made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                ann.loraine Ann Loraine made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]
                Mdavis4290 Molly Davis made changes -
                Summary Copy data to IGB Quickload host for visualization in IGB Copy KP 2023 data to IGB Quickload host for visualization in IGB
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                ann.loraine Ann Loraine added a comment - - edited

                Moving data onto new data.bioviz.org site with:

                local aloraine$ scp -J aloraine@hop.renci.org M1YNF4X1J.chr1.cram.crai aloraine@lorainelab-quickload.scidas.org:/projects/igbquickload/lorainelab/www/main/htdocs/genomesequence/H_sapiens_Dec_2013/.
M1YNF4X1J.chr1.cram.crai                                    100%  140KB 570.9KB/s   00:00
                Show
                ann.loraine Ann Loraine added a comment - - edited Moving data onto new data.bioviz.org site with: local aloraine$ scp -J aloraine@hop.renci.org M1YNF4X1J.chr1.cram.crai aloraine@lorainelab-quickload.scidas.org:/projects/igbquickload/lorainelab/www/main/htdocs/genomesequence/H_sapiens_Dec_2013/. M1YNF4X1J.chr1.cram.crai 100% 140KB 570.9KB/s 00:00
                ann.loraine Ann Loraine made changes -
                Summary Copy KP 2023 data to IGB Quickload host for visualization in IGB Copy KP 2023 data (30-804059537) to IGB Quickload host for visualization in IGB

                  People

                  • Assignee:
                    ann.loraine Ann Loraine
                    Reporter:
                    Mdavis4290 Molly Davis
                  • Votes:
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                    Watchers:
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                    Dates

                    • Created:
                      Updated:
                      Resolved: