mtruglio

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Jan 21st, 2021
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  1. #!/bin/bash
  2.  
  3. # The following block can be used by the job system
  4. # to ensure this script is runnable before actually attempting
  5. # to run it.
  6. if [ -n "$ABC_TEST_JOB_SCRIPT_INTEGRITY_XYZ" ]; then
  7.     exit 42
  8. fi
  9. [ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '/home/user/galaxy/database/dependencies/_conda/envs/mulled-v1-1fdf004bae7d448d7fc889acfdab5ae5aa1df6c114a660422dc114ed091c3e07')" ] || {
  10. MAX_TRIES=3
  11. COUNT=0
  12. while [ $COUNT -lt $MAX_TRIES ]; do
  13.     . '/home/user/galaxy/database/dependencies/_conda/bin/activate' '/home/user/galaxy/database/dependencies/_conda/envs/mulled-v1-1fdf004bae7d448d7fc889acfdab5ae5aa1df6c114a660422dc114ed091c3e07' > conda_activate.log 2>&1
  14.     if [ $? -eq 0 ];then
  15.         break
  16.     else
  17.         let COUNT=COUNT+1
  18.         if [ $COUNT -eq $MAX_TRIES ];then
  19.             echo "Failed to activate conda environment! Error was:"
  20.             cat conda_activate.log
  21.             exit 1
  22.         fi
  23.         sleep 10s
  24.     fi
  25. done
  26. } ; [ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '/home/user/galaxy/database/dependencies/_conda/envs/mulled-v1-1fdf004bae7d448d7fc889acfdab5ae5aa1df6c114a660422dc114ed091c3e07')" ] || {
  27. MAX_TRIES=3
  28. COUNT=0
  29. while [ $COUNT -lt $MAX_TRIES ]; do
  30.     . '/home/user/galaxy/database/dependencies/_conda/bin/activate' '/home/user/galaxy/database/dependencies/_conda/envs/mulled-v1-1fdf004bae7d448d7fc889acfdab5ae5aa1df6c114a660422dc114ed091c3e07' > conda_activate.log 2>&1
  31.     if [ $? -eq 0 ];then
  32.         break
  33.     else
  34.         let COUNT=COUNT+1
  35.         if [ $COUNT -eq $MAX_TRIES ];then
  36.             echo "Failed to activate conda environment! Error was:"
  37.             cat conda_activate.log
  38.             exit 1
  39.         fi
  40.         sleep 10s
  41.     fi
  42. done
  43. } ; python /home/user/galaxy/database/shed_tools/localhost/repos/admin/test_toy/ed1a21af8571/test_toy/testtoy.py '/home/user/galaxy/database/objects/8/6/c/dataset_86c6a42b-03ac-425d-afe5-be8c579afdc6.dat' > '/home/user/galaxy/database/objects/8/e/2/dataset_8e24d67e-a054-4f5f-89ff-09f63e64c6e5.dat'
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