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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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The script needs to take two options
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# the output json file name without the extension
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# input mrc file path
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* Within Leginon MosaicExternalScoreFinder instance defines, for each incoming gr image:
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Here is an example of this shell script we call sq_finding.sh
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<pre>
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#!/bin/sh -f
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# Local runs
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source /usr/local/anaconda3/etc/profile.d/conda.sh
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conda activate /opt/condaenvs/ptolemy_env
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# variable 1 is the outputname without json extension.
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# variable 2 is the input mrc path
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echo $1
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echo $2
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mrc_path=$2
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python /home/your_name/packages/ptolemy/lowmag_cli.py -f json $2 > $1
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conda deactivate
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# mv the result to leginon session rawdata directory
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mv $1 ${mrc_path%%rawdata/*}rawdata/$1.json
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echo ${mrc_path%%rawdata/*}rawdata/$1.json
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</pre>
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Test example, assuming you have /data/leginon/22feb28a/rawdata/22feb28a_00001gr.mrc, you can test ptolemy with
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<pre>
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./sq_finding.sh test_1 /data/leginon/22feb28a/rawdata/22feb28a_00001gr.mrc
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</pre>
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Output test_1.json should end up in /data/leginon/22feb28a/rawdata/