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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")

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              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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                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.
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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.
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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/.
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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
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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/
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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

                  People

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

                    • Created:
                      Updated:
                      Resolved: