autostart by systemd

sequenceserver
#1

Hi,

I need some help to autostart sequenceserver.

Sequenceserver is working when I launch the command from the shell and go to the web page but when I want to autostart with systemd, it’s not working.

In /var/log/messages, I have this output :

Nov 15 18:21:32 bio39 sequenceserver: download the correct package for itself. Please enter the path to NCBI BLAST+

Nov 15 18:21:32 bio39 sequenceserver: or press Enter to download.

Nov 15 18:21:32 bio39 sequenceserver: Press Ctrl+C to quit.

Nov 15 18:21:32 bio39 sequenceserver: Installing NCBI BLAST+.

Nov 15 18:21:32 bio39 sequenceserver: RUBY_PLATFORM x86_64-linux

Nov 15 18:21:32 bio39 sequenceserver: curl: Can’t open ‘/tmp/ncbi-blast-2.2.30±x64-linux.tar.gz’!

Nov 15 18:21:32 bio39 sequenceserver: curl: try ‘curl --help’ or ‘curl --manual’ for more information

Nov 15 18:21:32 bio39 systemd: sequenceserver.service: main process exited, code=exited, status=1/FAILURE

Nov 15 18:21:32 bio39 systemd: Unit sequenceserver.service entered failed state.

Nov 15 18:21:32 bio39 systemd: sequenceserver.service failed.

I don’t understand why sequenceserver want to open the tar gzip ncbi file while it doesn’t appear when sequenceserver is launch directly by command line.

I’ve created the user and the sequenceserver.service file and reload the daemon.

The command line in ExecStart is working when launched from the shell.

Thanks for your help,

Marine

#2

Hi Marine,

From what it looks like, the service daemon is not able to locate the

NCBI BLAST+ executable (and is trying to download and install them)
since most likely that are in your local path. You could specify the
path of the BLAST+ executables in your sequenceserver command using
the -b switch.

Let me know if it works.

Vivek

#3

I try the -b option in the command of ExecStart but it doesn’t work. I have a new error message:

[root@bio html]# systemctl status sequenceserver.service
● sequenceserver.service - SequenceServer server daemon
Loaded: loaded (/etc/systemd/system/sequenceserver.service; enabled; vendor preset: disabled)
Active: activating (auto-restart) (Result: exit-code) since mer. 2017-11-15 18:46:12 CET; 3s ago
Docs: file://sequenceserver --help
http://sequenceserver.com/doc
Process: 32337 ExecStart=/usr/local/bin/sequenceserver -c /root/.sequenceserver.conf -b /root/.sequenceserver/ncbi-blast-2.2.30+/bin (code=exited, status=1/FAILURE)
Main PID: 32337 (code=exited, status=1/FAILURE)

I already give this path in the sequenceserver.conf however :

:bin: /root/.sequenceserver/ncbi-blast-2.2.30+/bin
:database_dir: /var/www/html/sequenceserver

Thanks again :slight_smile:

#4

I forgot the log result:

#5

I found the answer: permission of access of folders needed to be changed.

Marine