====== irods ======
===== Database =====
We use postgres as the database, so lets's install it:
apt install postgresql-12
Create DB and user
psql (12.9 (Ubuntu 12.9-0ubuntu0.20.04.1))
Type "help" for help.
postgres=# CREATE USER irods WITH PASSWORD 'xxxx';
CREATE ROLE
postgres=# CREATE DATABASE "ICAT";
CREATE DATABASE
^
postgres=# GRANT ALL PRIVILEGES ON DATABASE "ICAT" TO irods;
GRANT
postgres=# \l
List of databases
Name | Owner | Encoding | Collate | Ctype | Access privileges
-----------+----------+----------+-------------+-------------+-----------------------
ICAT | postgres | UTF8 | en_GB.UTF-8 | en_GB.UTF-8 | =Tc/postgres +
| | | | | postgres=CTc/postgres+
| | | | | irods=CTc/postgres
postgres | postgres | UTF8 | en_GB.UTF-8 | en_GB.UTF-8 |
template0 | postgres | UTF8 | en_GB.UTF-8 | en_GB.UTF-8 | =c/postgres +
| | | | | postgres=CTc/postgres
template1 | postgres | UTF8 | en_GB.UTF-8 | en_GB.UTF-8 | =c/postgres +
| | | | | postgres=CTc/postgres
(4 rows)
===== Installing =====
No ubuntu 20.04 packages are available for 4.2.11 (expected in 4.3). But it looks like with a few older depednacies it can work. Taken from:
http://docs.snic.se/wiki/IRODS_iCommands_installation_on_Ubuntu_20.04
dejan@dejan:~$ LSB_RELEASE="bionic"
dejan@dejan:~$ wget -qO - https://packages.irods.org/irods-signing-key.asc | sudo apt-key add -
OK
dejan@dejan:~$ echo "deb [arch=amd64] https://packages.irods.org/apt/ ${LSB_RELEASE} main" \
> | sudo tee /etc/apt/sources.list.d/renci-irods.list
deb [arch=amd64] https://packages.irods.org/apt/ bionic main
dejan@dejan:~$ sudo apt-get update
Hit:1 http://se.archive.ubuntu.com/ubuntu focal InRelease
Hit:2 http://se.archive.ubuntu.com/ubuntu focal-updates InRelease
Hit:3 http://se.archive.ubuntu.com/ubuntu focal-backports InRelease
Hit:4 http://se.archive.ubuntu.com/ubuntu focal-security InRelease
Hit:5 https://packages.irods.org/apt bionic InRelease
Reading package lists... Done
dejan@dejan:~$
wget -c \
http://security.ubuntu.com/ubuntu/pool/main/p/python-urllib3/python-urllib3_1.22-1ubuntu0.18.04.2_all.deb \
http://security.ubuntu.com/ubuntu/pool/main/r/requests/python-requests_2.18.4-2ubuntu0.1_all.deb \
http://security.ubuntu.com/ubuntu/pool/main/o/openssl1.0/libssl1.0.0_1.0.2n-1ubuntu5.7_amd64.deb \
http://security.ubuntu.com/ubuntu/pool/main/p/python-jsonschema/python-jsonschema_2.6.0-2_all.deb \
http://security.ubuntu.com/ubuntu/pool/main/p/python-functools32/python-functools32_3.2.3.2-3_all.deb
sudo apt install \
./python-urllib3_1.22-1ubuntu0.18.04.2_all.deb \
./python-requests_2.18.4-2ubuntu0.1_all.deb \
./libssl1.0.0_1.0.2n-1ubuntu5.7_amd64.deb \
./python-jsonschema_2.6.0-2_all.deb \
./python-functools32_3.2.3.2-3_all.deb
rm -rf \
./python-urllib3_1.22-1ubuntu0.18.04.2_all.deb \
./python-requests_2.18.4-2ubuntu0.1_all.deb \
./libssl1.0.0_1.0.2n-1ubuntu5.7_amd64.deb \
./python-jsonschema_2.6.0-2_all.deb \
./python-functools32_3.2.3.2-3_all.deb
$ sudo apt-get install irods-server irods-database-plugin-postgres
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following additional packages will be installed:
irods-externals-avro1.9.0-0 irods-externals-boost1.67.0-0 irods-externals-clang-runtime6.0-0 irods-externals-fmt6.1.2-1
irods-externals-libarchive3.3.2-1 irods-externals-nanodbc2.13.0-1 irods-externals-zeromq4-14.1.6-0 irods-icommands irods-runtime
libodbc1 odbc-postgresql odbcinst odbcinst1debian2 python-psutil super
Suggested packages:
libmyodbc tdsodbc unixodbc-bin python-psutil-doc
The following NEW packages will be installed:
irods-database-plugin-postgres irods-externals-avro1.9.0-0 irods-externals-boost1.67.0-0 irods-externals-clang-runtime6.0-0
irods-externals-fmt6.1.2-1 irods-externals-libarchive3.3.2-1 irods-externals-nanodbc2.13.0-1 irods-externals-zeromq4-14.1.6-0
irods-icommands irods-runtime irods-server libodbc1 odbc-postgresql odbcinst odbcinst1debian2 python-psutil super
0 upgraded, 17 newly installed, 0 to remove and 0 not upgraded.
Need to get 37.5 MB of archives.
After this operation, 255 MB of additional disk space will be used.
Do you want to continue? [Y/n]
But get this error:
Unpacking irods-icommands (4.2.11-1~bionic) ...
dpkg: error processing archive /tmp/apt-dpkg-install-l8YKdz/14-irods-icommands_4.2.11-1~bionic_amd64.deb (--unpack):
trying to overwrite '/usr/bin/ils', which is also in package sleuthkit 4.6.7-1build1
dpkg-deb: error: paste subprocess was killed by signal (Broken pipe)
Selecting previously unselected package irods-server.
Preparing to unpack .../15-irods-server_4.2.11-1~bionic_amd64.deb ...
Unpacking irods-server (4.2.11-1~bionic) ...
Selecting previously unselected package irods-database-plugin-postgres.
Preparing to unpack .../16-irods-database-plugin-postgres_4.2.11-1~bionic_amd64.deb ...
Unpacking irods-database-plugin-postgres (4.2.11-1~bionic) ...
Errors were encountered while processing:
/tmp/apt-dpkg-install-l8YKdz/14-irods-icommands_4.2.11-1~bionic_amd64.deb
E: Sub-process /usr/bin/dpkg returned an error code (1)
Let's overwrite it:
$ sudo apt install --fix-broken -o Dpkg::Options::="--force-overwrite"
Reading package lists... Done
Building dependency tree
Reading state information... Done
Correcting dependencies... Done
The following additional packages will be installed:
irods-icommands
The following NEW packages will be installed:
irods-icommands
0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
16 not fully installed or removed.
Need to get 0 B/1,333 kB of archives.
After this operation, 4,573 kB of additional disk space will be used.
Do you want to continue? [Y/n]
(Reading database ... 513208 files and directories currently installed.)
Preparing to unpack .../irods-icommands_4.2.11-1~bionic_amd64.deb ...
Unpacking irods-icommands (4.2.11-1~bionic) ...
dpkg: warning: overriding problem because --force enabled:
dpkg: warning: trying to overwrite '/usr/bin/ils', which is also in package sleuthkit 4.6.7-1build1
dpkg: warning: overriding problem because --force enabled:
dpkg: warning: trying to overwrite '/usr/share/man/man1/ils.1.gz', which is also in package sleuthkit 4.6.7-1build1
Setting up irods-externals-avro1.9.0-0 (1.0~bionic) ...
Setting up irods-externals-zeromq4-14.1.6-0 (1.0~bionic) ...
Setting up irods-externals-libarchive3.3.2-1 (1.0~bionic) ...
Setting up irods-externals-clang-runtime6.0-0 (1.0~bionic) ...
Setting up super (3.30.1-1) ...
Setting up libodbc1:amd64 (2.3.6-0.1build1) ...
Setting up python-psutil (5.5.1-1ubuntu4) ...
Setting up irods-externals-fmt6.1.2-1 (1.0~bionic) ...
Setting up irods-externals-boost1.67.0-0 (1.0~bionic) ...
Setting up irods-externals-nanodbc2.13.0-1 (1.0~bionic) ...
Setting up irods-runtime (4.2.11-1~bionic) ...
Setting up irods-icommands (4.2.11-1~bionic) ...
Setting up irods-server (4.2.11-1~bionic) ...
Setting up odbcinst (2.3.6-0.1build1) ...
Setting up odbcinst1debian2:amd64 (2.3.6-0.1build1) ...
Setting up odbc-postgresql:amd64 (1:12.01.0000-1) ...
grep: /etc/odbcinst.ini: No such file or directory
odbcinst: Driver installed. Usage count increased to 1.
Target directory is /etc
odbcinst: Driver installed. Usage count increased to 1.
Target directory is /etc
Setting up irods-database-plugin-postgres (4.2.11-1~bionic) ...
=======================================================================
iRODS Database Plugin installation was successful.
To configure this plugin, the following prerequisites need to be met:
- an existing database user (to be used by the iRODS server)
- an existing database (to be used as the iCAT catalog)
- permissions for existing user on existing database
Then run the following setup script:
sudo python /var/lib/irods/scripts/setup_irods.py
=======================================================================
Processing triggers for man-db (2.9.1-1) ...
Processing triggers for libc-bin (2.31-0ubuntu9.2) ...
Processing triggers for systemd (245.4-4ubuntu3.15) ...