Setup Ptolemy CLI shell script » History » Version 1
Anchi Cheng, 03/01/2022 12:48 AM
1 | 1 | Anchi Cheng | h1. Setup Ptolemy CLI shell script |
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3 | The script needs to take two options |
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5 | # the output json file name without the extension |
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6 | # input mrc file path |
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8 | * Within Leginon MosaicExternalScoreFinder instance defines, for each incoming gr image: |
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10 | Here is an example of this shell script we call sq_finding.sh |
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12 | <pre> |
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13 | #!/bin/sh -f |
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14 | # Local runs |
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15 | source /usr/local/anaconda3/etc/profile.d/conda.sh |
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16 | conda activate /opt/condaenvs/ptolemy_env |
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17 | # variable 1 is the outputname without json extension. |
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18 | # variable 2 is the input mrc path |
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19 | echo $1 |
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20 | echo $2 |
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21 | mrc_path=$2 |
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22 | python /home/your_name/packages/ptolemy/lowmag_cli.py -f json $2 > $1 |
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23 | conda deactivate |
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24 | # mv the result to leginon session rawdata directory |
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25 | mv $1 ${mrc_path%%rawdata/*}rawdata/$1.json |
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26 | echo ${mrc_path%%rawdata/*}rawdata/$1.json |
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27 | </pre> |
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29 | Test example, assuming you have /data/leginon/22feb28a/rawdata/22feb28a_00001gr.mrc, you can test ptolemy with |
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30 | <pre> |
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31 | ./sq_finding.sh test_1 /data/leginon/22feb28a/rawdata/22feb28a_00001gr.mrc |
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32 | </pre> |
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33 | Output test_1.json should end up in /data/leginon/22feb28a/rawdata/ |