scipion-em-ispyb 1.0.0

ISPyB monitor for scipion

ISPYB MONITOR

This plugin contains a monitor to send data to an ISPyB database, so having a working ISPyB database is required. Below we summarize the steps taken to test this plugin if you don’t already have ISPyB.

Setup

• Install MariaDB: Download choosing OS and version (recommended >=10.2), follow steps: https://downloads.mariadb.org/mariadb/repositories/#mirror=digitalocean-sfo&distro=Ubuntu&distro_release=xenial–ubuntu_xenial&version=10.3

• Fix root login: check if you can log in as root to mysql ( $mysql -u root -p ).Skip this step if you log in successfully.If not, use the accepted answer on this link to fix your root login: https://askubuntu.com/questions/705458/ubuntu-15-10-mysql-error-1524-unix-socket.

• Log in as root:

$mysql -u root -p

• Set log_bin_trust_function_creators:

MariaDB [(none)]> set global log_bin_trust_function_creators=ON;
Query OK, 0 rows affected (0.000 sec)

• Create DB:

MariaDB [(none)]> create database ispyb;
Query OK, 1 row affected (0.000 sec)

• Create user for DB: Grant privileges to your user on ispyb database we just created. See https://stackoverflow.com/questions/5016505/grant-all-privileges-on-database . Here we create a user username that can log in without password.

MariaDB [(none)]> CREATE USER username;
MariaDB [(none)]> CREATE USER username@’localhost’;
MariaDB [(none)]> use ispyb
MariaDB [(ispyb)]> GRANT ALL PRIVILEGES ON ispyb.* to username@'localhost';
MariaDB [(ispyb)]> grant all privileges on ispyb.* to username@'%';

• Add schemas: Clone this repository and follow steps to add schemas https://github.com/DiamondLightSource/ispyb-database

• Create a config file: based on https://github.com/DiamondLightSource/ispyb-api/blob/master/conf/config.example.cfg

[ispyb_mysql_sp]
user = username
pw =
host = localhost
port = 3306
db = ispyb

• Set ISPYB_CONFIG: you can do it in the terminal where you will launch Scipion doing export ISPYB_CONFIG=path/to/ispyb.cfg or set it in the variables section of ~/.config/scipion/scipion.conf)

[VARIABLES]
SCIPION_NOTES_PROGRAM =
SCIPION_NOTES_ARGS =
SCIPION_NOTES_FILE = notes.txt
SCIPION_NOTIFY = False
ISPYB_CONFIG=/path/to/ispyb.conf

• Install this plugin:

scipion installp -p scipion-em-ispyb

Alternatively, in devel mode:

scipion installp -p local/path/to/scipion-em-ispyb --devel

Run and test

• Run Scipion and the ISPyB monitor: you should now be able to find the ISPyB monitor in the list of available protocols of Scipion. Launch a workflow with one or all of the following protocols: import movies,movie alignment, ctf estimation (TestStreamingWorkflow is a good candidate), and set them as the input of ISPyB Monitor. For test purposes, you can select “test” as the database in the dropdown menu at the bottom, and use cm14451-2 as the visit.

• ISPyB import error: If the monitor fails because it can’t import bz2, we need to install in our system libbz2-dev and re-install Scipion:

sudo apt-get install libbz2-dev
rm -rf software/lib/*
rm -rf software/include/*
rm software/bin/*
scipion install -j 8

• Check the data in the ISPyB database:

MariaDB [ispyb]> select micrographFullPath, movieId, totalMotion from MotionCorrection;
+--------------------------------------------------------------+---------+-------------+
| micrographFullPath                                           | movieId | totalMotion |
+--------------------------------------------------------------+---------+-------------+
| Runs/000615_ProtMotionCorr/extra/movie000001_aligned_mic.mrc |       1 |     1.96068 |
| Runs/000615_ProtMotionCorr/extra/movie000002_aligned_mic.mrc |       2 |     3.57892 |
| Runs/000615_ProtMotionCorr/extra/movie000003_aligned_mic.mrc |       3 |     2.17066 |
| Runs/000615_ProtMotionCorr/extra/movie000004_aligned_mic.mrc |       4 |     1.96068 |
| Runs/000615_ProtMotionCorr/extra/movie000005_aligned_mic.mrc |       5 |     3.57892 |
| Runs/000615_ProtMotionCorr/extra/movie000006_aligned_mic.mrc |       6 |     2.17066 |
| Runs/000615_ProtMotionCorr/extra/movie000007_aligned_mic.mrc |       7 |     1.96068 |
| Runs/000615_ProtMotionCorr/extra/movie000008_aligned_mic.mrc |       8 |     3.57892 |
| Runs/000615_ProtMotionCorr/extra/movie000009_aligned_mic.mrc |       9 |     2.17066 |