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  • At the end of the job script, you must add instruction to copy the results of your analysis back to /pool(or /scratch, or /data).

    If/when the results are easily identifiable, you can use the commands mv or tar,  and find, here are a few examples:


    1. Move the directory where all the results are stored and the log file, delete the rest.

      Code Block
      languagebash
      titlemoving identifiable results, delete the rest
      # move results and log file back
      cd $SSD_DIR
      mv results /pool/genomics/smart1/great/project/wild-cat/.
      mv wow.log /pool/genomics/smart1/great/project/wild-cat/.
      #
      # delete the rest
      rm -rf *


    2. Move the directory where all the results are stored and the log file, delete the input (conservative approach, in case you missed something).

      Code Block
      languagebash
      titlemoving identifiable results, delete known input sets
      Code Block
      languagebash
      # move results and log file back
      cd $SSD_DIR
      mv results /pool/genomics/smart1/great/project/wild-cat/.
      mv wow.log /pool/genomics/smart1/great/project/wild-cat/.
      #
      # delete input set and other stuff
      rm -rf input
      rm wow.gen wow.conf


    3. ove Move using the --update flag of mv (see man mv)

      Code Block
      languagebash
      titlemoving using --update
      Code Block
      languagebash
      
      # move results using --update
      cd $SSD_DIR
      mv --update * /pool/genomics/smart1/great/project/wild-cat/.
      #
      # delete the rest
      rm -rf *

       Note, you can use mv --update on an explicit list (of files, directories, or file specification), not just * (everything), and you do not have to remove the rest,  but can only remove what you know you can safely remove (conservative approach).
       

    4. ind Find newer files and move them: the trick is to create a 'timestamp' file before starting the analysis.
       That file can be used later to find any newer file with the --newer= option of tar (see man tar):

      Code Block
      languagebash
      titleUsing a timestamp file and tar --newer=
      Code Block
      languagebash
      # set the timestamp
      date > $SSD_DIR/started.txt
      # run the analysis
      ...
      # copy the new files in the subdir data/ to a compressed tar-ball
      cd $SSD_DIR
      tar --newer=$SSD_DIR/started.txt -cfz /pool/genomics/smart1/great/project/wild-cat-results.tgz data/
      # now remove it
      rm -rf data/
      # etc...
      # delete everything, unless
      rm -rf *

      See previous comments and what to tar and what to remove: once you've tar'd new stuff in data/,  remove data/, etc.

    5. Using the timestamp file and  the find command (see man find):

      Code Block
      languagebash
      titleUsing find and a timestamp file
      Code Block
      languagebash
      # set the timestamp
      date > $SSD_DIR/started.txt
      # run the analysis
      ...
      # find the new files in the subdir data/
      cd $SSD_DIR
      find data/ -newer $SSD_DIR/started.txt -type f > /tmp/list
      # do the same on logs/, append to the list
      find logs/ -newer $SSD_DIR/started.txt -type f >> /tmp/list
      # etc...
      # now save what is in the list with one tar
      tar --files-from=/tmp/list -cfz /pool/genomics/smart1/great/project/wild-cat-results.tgz data/
      # now remove data/ and logs/
      rm -rf data/ logs/
      # etc...
      # delete everything, unless
      rm -rf *


      (lightbulb) BTW, the advantage of writing a .tgz file, rather than moving files is two fold, assuming your stuff is compressible:(tick) There are many more ways to accomplish this ....

      1. You write less in the .tgz file, so it should be done faster (reading and compressing should be fast, writing is the slow step)

      2. you need less disk space for your output (since it is compressed).

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