Change /tmp for sequenceserver

sequenceserver
#1

Hello,

I am trying to change the default directory where sequenceserver writes file from /tmp to some folder in home directory.

I searched forum, and followed some instructions.

I tried to change config.ru file

cat /usr/local/share/gems/gems/sequenceserver-1.0.11/config.ru

require ‘sequenceserver’

def Dir.tmpdir

‘/home/AM_assembly/tmp’

end

SequenceServer.init

run SequenceServer

I also set $TMPDIR

But it didn’t help.

Could you advise something

sequenceserver -v

1.0.11

Thank you,
Nataliya

#2

Hi Nataliya,

If you are launching SequenceServer from command line, the following works:

TMPDIR=/path sequenceserver

config.ru is relevant only if you are using SequenceServer with Apache. Your code does look like it should work. Alternatively, I have the following at the top of one of my old config.ru file:

ENV[’TMPDIR’]=/path

Note that temporary files are deleted once they have been used.

Priyam

#3

Thank you Priyam,

unfortunately none of this worked

The temporary files are deleted indeed after sequence server stops, if pressing CTRL+C,
but I have sequence server in Autorun

cat /etc/systemd/system/multi-user.target.wants/sequenceserver.service

[Unit]

Description=SequenceServer server daemon

Documentation=“file://sequenceserver --help” “http://sequenceserver.com/doc”

After=network.target

[Service]

Type=simple

User=AM_assembly

ExecStart=/usr/local/bin/sequenceserver -c /home/AM_assembly/.sequenceserver.conf

KillMode=process

Restart=on-failure

RestartSec=42s

RestartPreventExitStatus=255

[Install]

WantedBy=multi-user.target

I
so files stay in /tmp all the time until I delete them manually, for example
In /tmp

-rw------- 1 AM_assembly AM_assembly 1.8K Mar 31 19:36 sequenceserver_query20200331-69120-qm9hv9

-rw------- 1 AM_assembly AM_assembly 1.8K Mar 31 19:54 sequenceserver_query20200331-69120-qp5vjp

-rw------- 1 AM_assembly AM_assembly 843 Mar 31 19:19 sequenceserver_query20200331-69120-scj86d

-rw------- 1 AM_assembly AM_assembly 843 Mar 31 18:56 sequenceserver_query20200331-69120-zaj3p5

-rw------- 1 AM_assembly AM_assembly 0 Apr 1 06:46 sequenceserver_query20200401-69120-15as5ex

-rw------- 1 AM_assembly AM_assembly 0 Apr 1 08:53 sequenceserver_query20200401-69120-1hi4vi1

-rw------- 1 AM_assembly AM_assembly 0 Apr 1 06:47 sequenceserver_query20200401-69120-1sxk5dy

-rw------- 1 AM_assembly AM_assembly 4.0K Apr 1 10:19 sequenceserver_query20200401-69120-9jdv5c

-rw------- 1 AM_assembly AM_assembly 2.1K Apr 1 11:52 sequenceserver_query20200401-69120-h3o8zo

when some big searched are launched files can grow to Gbs and we ended up with no space in /

that’s why I am looking for possibility to change /tmp

What else I can try? Or maybe I am doing something wrong?

чт, 2 апр. 2020 г. в 10:35, Anurag Priyam <anurag08priyam@gmail.com>:

#4

Is that a systemd unit file? What if you set TMPDIR environment variable using Environment directive:

Environment=TMPDIR=/path

That would go in the [Service] section.

See https://coreos.com/os/docs/latest/using-environment-variables-in-systemd-units.html

If that doesn’t work you can just create a little script, say ’sequenceserver.sh’, containing:

TMPDIR=/path sequenceserver -c …

And then change ExecStart to point to this script (absolute path).

If none of the above works, you can try to directly modify the code. There should be a lib folder next to the config.ru file you found earlier. Add the following at the top of lib/sequenceserver.rb

ENV[’TMPDIR’]=/path

#5

Nope, nothing worked again :frowning: sorry

When I run from command line line
TMPDIR=/path sequenceserver -c …

it doen’t work also, it seems that it is not reading TMPDIR at all.
Where is directory for temporary file defined in the code? Where are the instruction to read $TMPDIR?

чт, 2 апр. 2020 г. в 12:29, Anurag Priyam <anurag08priyam@gmail.com>:

#6

It is part of Ruby programming language’s standard library.

Priyam