Leginon

When rawtransfer.py checked out from git repository, the mode should already be set as 755.

So, this is what it looks like in the git clone:

cnsit@kraken:~/leginon/myami-beta/leginon$  ls -l raw*
-rwxrwxr-x 1 cnsit cnsit 19276 Nov 29 12:52 rawtransfer.py

However,

# ./pysetup.sh install

appears to have copied it over to $PYTHONSITEPKG without the +x:

root@kraken:/usr/local/lib/python2.7/dist-packages/leginon# ls -l rawtransfer.py
-rw-r--r-- 1 root root 19276 Nov 29 12:52 rawtransfer.py

I see.

What you may want to do is to copy rawtransfer.py to somewhere you can access from your $PATH environment variable because just being executable is not enough to find it. I do not think it makes sense for $PATH environment variable to look for files in the dist-packages directory. This is similar to start-leginon.py and appion directories.

Thanks for pointing this out. I will make changes in the setup.py as well as wiki.

OK, here is a systemd solution that works. It would be more elegant using Environment directives, but these don't seem to be supported by the version of systemd that ships with Ubuntu 16.04. Note that if you're still on CentOS 6, this won't work for you, but should be fine on CentOS 7. The added bonus is that rawtransfer.py is restarted automatically if it crashes or dies.

Create a file in /etc/systemd/system which ends in .service (we have 2 microscopes, so there is a service file for each microscope; e.g. rawtransfer-krios.service)

[Unit]
Description=rawtransfer.py service for Krios
After=network.target

[Service]
Type=simple
Restart=on-failure
User=root
Group=root

ExecStart=/usr/local/lib/python2.7/dist-packages/leginon/rawtransfer.py --method=rsync --source_path=/cryodata/krios-k2-frames --camera_host=krios-k2 --destination_head=/cryodata 2>&1 >/var/log/rawtransfer-krios-k2.log

[Install]
WantedBy=multi-user.target

Start/Stop the service by typing:

systemctl start rawtransfer-krios
systemctl stop rawtransfer-krios

To set rawtransfer.py to start automatically when the system boots:

systemctl enable rawtransfer-krios

Created Issue #5445. See the python installator solution there.