Setup Ptolemy CLI shell script » History » Revision 2
Revision 1 (Anchi Cheng, 03/01/2022 12:48 AM) → Revision 2/5 (Anchi Cheng, 03/15/2022 12:53 PM)
h1. Setup Ptolemy CLI shell script for Square Finding
The script needs to take two options
# the output json file name without the extension
# input mrc file path
* Within Leginon MosaicExternalScoreFinder instance defines, for each incoming gr image:
Here is an example of this shell script we call sq_finding.sh
<pre>
#!/bin/sh -f
# Local runs
source /usr/local/anaconda3/etc/profile.d/conda.sh
conda activate /opt/condaenvs/ptolemy_env
# variable 1 is the outputname without json extension.
# variable 2 is the input mrc path
echo $1
echo $2
mrc_path=$2
python /home/your_name/packages/ptolemy/lowmag_cli.py -f json $2 > $1
conda deactivate
# mv the result to leginon session rawdata directory
mv $1 ${mrc_path%%rawdata/*}rawdata/$1.json
echo ${mrc_path%%rawdata/*}rawdata/$1.json
</pre>
Test example, assuming you have /data/leginon/22feb28a/rawdata/22feb28a_00001gr.mrc, you can test ptolemy with
<pre>
./sq_finding.sh test_1 /data/leginon/22feb28a/rawdata/22feb28a_00001gr.mrc
</pre>
Output test_1.json should end up in /data/leginon/22feb28a/rawdata/