Difference between revisions of "IRODS iCommands installation on Ubuntu 16.04"

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(List available packages)
(Authenticate and test iRODS iCommands client)
 
(3 intermediate revisions by the same user not shown)
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'''Back to [https://snicdocs.nsc.liu.se/wiki/Swestore-iRODS Swestore-iRODS Documentation]'''
  
 
== Install the public key and add the repository ==
 
== Install the public key and add the repository ==
Line 241: Line 243:
 
  vitlacil@host:~$  
 
  vitlacil@host:~$  
 
   
 
   
 +
== Configure the iRODS environment ==
 +
 +
NOTE: Create your own configuration file !!
 +
 +
vitlacil@host:~$ cd /home/vitlacil/
 +
vitlacil@host:~$ mkdir .irods
 +
vitlacil@host:~$ cat /home/vitlacil/.irods/irods_environment.json
 +
{
 +
  "irods_host": "irods-login.swestore.se",
 +
  "irods_port": 2432,
 +
  "irods_default_resource": "pdc-gpfs",
 +
  "irods_home": "/snic.se/home/s_dejvi",
 +
  "irods_cwd": "/snic.se/home/s_dejvi",
 +
  "irods_user_name": "s_dejvi",
 +
  "irods_zone_name": "snic.se",
 +
  "irods_client_server_negotiation": "request_server_negotiation",
 +
  "irods_client_server_policy": "CS_NEG_REFUSE",
 +
  "irods_default_hash_scheme": "SHA256",
 +
  "irods_encryption_algorithm": "AES-256-CBC",
 +
  "irods_encryption_key_size": 32,
 +
  "irods_encryption_num_hash_rounds": 16,
 +
  "irods_encryption_salt_size": 8,
 +
  "irods_match_hash_policy": "compatible",
 +
  "irods_authentication_scheme" : "PAM"
 +
}
  
vitlacil@host:~$
+
== Authenticate and test iRODS iCommands client ==
vitlacil@host:~$ ienv
+
  vitlacil@host:~$ iinit
  ERROR: environment_properties::capture: missing environment file. should be at [/home/vitlacil/.irods/irods_environment.json]
+
Enter your current PAM password:
irods_version - 4.2.7
+
vitlacil@host:~$ ils
vitlacil@host:~$ touch /home/vitlacil/.irods/irods_environment.json
+
/snic.se/home/s_dejvi:
touch: cannot touch '/home/vitlacil/.irods/irods_environment.json': No such file or directory
 
vitlacil@host:~$ vi /home/vitlacil/.irods/irods_environment.json
 
vitlacil@host:~$ sudo vi /home/vitlacil/.irods/irods_environment.json
 
vitlacil@host:~$ sudo vim /home/vitlacil/.irods/irods_environment.json
 
sudo: vim: command not found
 
vitlacil@host:~$ sudo apt install vim
 
Reading package lists... Done
 
Building dependency tree     
 
Reading state information... Done
 
The following additional packages will be installed:
 
  vim-runtime
 
Suggested packages:
 
  ctags vim-doc vim-scripts vim-gnome-py2 | vim-gtk-py2 | vim-gtk3-py2
 
  | vim-athena-py2 | vim-nox-py2
 
The following NEW packages will be installed:
 
  vim vim-runtime
 
0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded.
 
Need to get 6 205 kB of archives.
 
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Get:1 http://caesar.ftp.acc.umu.se/ubuntu xenial-updates/main amd64 vim-runtime all 2:7.4.1689-3ubuntu1.4 [5 169 kB]
 
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Adding 'diversion of /usr/share/vim/vim74/doc/help.txt to /usr/share/vim/vim74/doc/help.txt.vim-tiny by vim-runtime'
 
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Processing triggers for man-db (2.7.5-1) ...
 
Setting up vim-runtime (2:7.4.1689-3ubuntu1.4) ...
 
Setting up vim (2:7.4.1689-3ubuntu1.4) ...
 
update-alternatives: using /usr/bin/vim.basic to provide /usr/bin/vim (vim) in auto mode
 
update-alternatives: using /usr/bin/vim.basic to provide /usr/bin/vimdiff (vimdiff) in auto mode
 
update-alternatives: using /usr/bin/vim.basic to provide /usr/bin/rvim (rvim) in auto mode
 
update-alternatives: using /usr/bin/vim.basic to provide /usr/bin/rview (rview) in auto mode
 
update-alternatives: using /usr/bin/vim.basic to provide /usr/bin/vi (vi) in auto mode
 
update-alternatives: using /usr/bin/vim.basic to provide /usr/bin/view (view) in auto mode
 
update-alternatives: using /usr/bin/vim.basic to provide /usr/bin/ex (ex) in auto mode
 
vitlacil@host:~$
 
vitlacil@host:~$
 
vitlacil@host:~$
 
vitlacil@host:~$
 
vitlacil@host:~$ sudo vim /home/vitlacil/.irods/irods_environment.json
 
vitlacil@host:~$ sudo vim /home/vitlacil/.irods/irods_environment.json
 
vitlacil@host:~$ vim /home/vitlacil/.irods/irods_environment.json
 
vitlacil@host:~$
 
vitlacil@host:~$ ls /home/vitlacil/.irods/irods_environment.json
 
ls: cannot access '/home/vitlacil/.irods/irods_environment.json': No such file or directory
 
vitlacil@host:~$ gnome-open /home/vitlacil/.irods/irods_environment.json
 
The program 'gnome-open' is currently not installed. You can install it by typing:
 
sudo apt install libgnome2-bin
 
vitlacil@host:~$ vi /home/vitlacil/.irods/irods_environment.json
 
vitlacil@host:~$
 
vitlacil@host:~$
 
vitlacil@host:~$ cd /home/vitlacil/
 
vitlacil@host:~$
 
vitlacil@host:~$ mkdir .irods
 
vitlacil@host:~$ vi /home/vitlacil/.irods/irods_environment.json
 
vitlacil@host:~$
 
vitlacil@host:~$
 
vitlacil@host:~$
 
vitlacil@host:~$
 
vitlacil@host:~$ iinit
 
Enter your current PAM password:
 
vitlacil@host:~$ ils
 
/snic.se/home/s_dejvi:
 
 
   .DS_Store
 
   .DS_Store
 
   ._.DS_Store
 
   ._.DS_Store
Line 324: Line 281:
 
   C- /snic.se/home/s_dejvi/0 TiddlyWiki
 
   C- /snic.se/home/s_dejvi/0 TiddlyWiki
 
   C- /snic.se/home/s_dejvi/0 reading
 
   C- /snic.se/home/s_dejvi/0 reading
  C- /snic.se/home/s_dejvi/Dropbox
 
 
   C- /snic.se/home/s_dejvi/EOSC
 
   C- /snic.se/home/s_dejvi/EOSC
  C- /snic.se/home/s_dejvi/EOSC-Hub Reporting
 
 
   C- /snic.se/home/s_dejvi/EUDAT
 
   C- /snic.se/home/s_dejvi/EUDAT
 
   C- /snic.se/home/s_dejvi/FAIR
 
   C- /snic.se/home/s_dejvi/FAIR
 
   C- /snic.se/home/s_dejvi/FitSM
 
   C- /snic.se/home/s_dejvi/FitSM
   C- /snic.se/home/s_dejvi/Googletakeout
+
   .....
  C- /snic.se/home/s_dejvi/Magazines
+
vitlacil@host:~$
  C- /snic.se/home/s_dejvi/PIDs
+
 
  C- /snic.se/home/s_dejvi/Private
+
'''Back to [https://snicdocs.nsc.liu.se/wiki/Swestore-iRODS Swestore-iRODS Documentation]'''
  C- /snic.se/home/s_dejvi/Public
 
  C- /snic.se/home/s_dejvi/SNIC ALL HANDS 2019
 
  C- /snic.se/home/s_dejvi/SNIC Storage
 
  C- /snic.se/home/s_dejvi/Security
 
  C- /snic.se/home/s_dejvi/WebDAV test
 
  C- /snic.se/home/s_dejvi/iRODS
 
  C- /snic.se/home/s_dejvi/nordic data services workshop da aggiungere in AFS
 
  C- /snic.se/home/s_dejvi/test.from.klemming
 
vitlacil@host:~$
 

Latest revision as of 20:57, 6 May 2020

Back to Swestore-iRODS Documentation

Install the public key and add the repository

vitlacil@host:~$ wget -qO - https://packages.irods.org/irods-signing-key.asc | sudo apt-key add -
[sudo] password for vitlacil: *************************
OK
vitlacil@host:~$ wget -qO - https://packages.irods.org/irods-signing-key.asc | sudo apt-key add -
OK
vitlacil@host:~$ echo "deb [arch=amd64] https://packages.irods.org/apt/ $(lsb_release -sc) main" | sudo tee /etc/apt/sources.list.d/renci-irods.list
deb [arch=amd64] https://packages.irods.org/apt/ xenial main
vitlacil@host:~$ sudo apt-get update
Hit:1 http://se.archive.ubuntu.com/ubuntu xenial InRelease
Hit:2 http://se.archive.ubuntu.com/ubuntu xenial-updates InRelease             
Hit:3 http://se.archive.ubuntu.com/ubuntu xenial-backports InRelease           
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Get:5 https://packages.irods.org/apt xenial InRelease [3 499 B]                
Get:6 http://security.ubuntu.com/ubuntu xenial-security/main amd64 DEP-11 Metadata [76,7 kB]
Get:7 https://packages.irods.org/apt xenial/main amd64 Packages [31,8 kB]
Get:8 http://security.ubuntu.com/ubuntu xenial-security/universe amd64 DEP-11 Metadata [124 kB]
Get:9 http://security.ubuntu.com/ubuntu xenial-security/multiverse amd64 DEP-11 Metadata [2 464 B]
Fetched 348 kB in 1s (306 kB/s)                                            
Reading package lists... Done

List available packages

vitlacil@host:~$ apt-cache search irods
php-irods-prods - PHP client API for iRODS
irods-auth-plugin-gsi - The integrated Rule-Oriented Data System
irods-auth-plugin-krb - The integrated Rule-Oriented Data System
irods-database-plugin-mysql - The integrated Rule-Oriented Data System
irods-database-plugin-oracle - The integrated Rule-Oriented Data System
irods-database-plugin-postgres - The integrated Rule-Oriented Data System
irods-dev - The integrated Rule-Oriented Data System
irods-externals-autoconf5ad3567c-0 - iRODS Build Dependency
irods-externals-avro1.7.7-0 - iRODS Build Dependency
irods-externals-avro1.8.2-0 - iRODS Build Dependency
irods-externals-avro1.9.0-0 - iRODS Build Dependency
irods-externals-aws-sdk-cpp1.4.89-0 - iRODS Build Dependency
irods-externals-aws-sdk-cpp1.4.89-1 - iRODS Build Dependency
irods-externals-boost1.60.0-0 - iRODS Build Dependency
irods-externals-boost1.67.0-0 - iRODS Build Dependency
irods-externals-catch22.3.0-0 - iRODS Build Dependency
irods-externals-clang3.8-0 - iRODS Build Dependency
irods-externals-clang6.0-0 - iRODS Build Dependency
irods-externals-clang-runtime3.8-0 - iRODS Build Dependency
irods-externals-clang-runtime6.0-0 - iRODS Build Dependency
irods-externals-cmake3.5.2-0 - iRODS Build Dependency
irods-externals-cmake3.11.4-0 - iRODS Build Dependency
irods-externals-cppzmq4.1-0 - iRODS Build Dependency
irods-externals-cppzmq4.2.3-0 - iRODS Build Dependency
irods-externals-cpr1.3.0-0 - iRODS Build Dependency
irods-externals-cpr1.3.0-1 - iRODS Build Dependency
irods-externals-elasticlient0.1.0-0 - iRODS Build Dependency
irods-externals-elasticlient0.1.0-1 - iRODS Build Dependency
irods-externals-epm4.2-0 - iRODS Build Dependency
irods-externals-fmt6.1.2-0 - iRODS Build Dependency
irods-externals-fmt6.1.2-1 - iRODS Build Dependency
irods-externals-imagemagick7.0.3-0 - iRODS Build Dependency
irods-externals-imagemagick7.0.8-0 - iRODS Build Dependency
irods-externals-jansson2.7-0 - iRODS Build Dependency
irods-externals-json3.0.1-0 - iRODS Build Dependency
irods-externals-json3.1.2-0 - iRODS Build Dependency
irods-externals-json3.7.3-0 - iRODS Build Dependency
irods-externals-libarchive3.1.2-0 - iRODS Build Dependency 
irods-externals-libarchive3.3.2-0 - iRODS Build Dependency
irods-externals-libarchive3.3.2-1 - iRODS Build Dependency
irods-externals-libs3a30e55e8-0 - iRODS Build Dependency
irods-externals-libs3a30e55e8-1 - iRODS Build Dependency
irods-externals-libs359b62371-0 - iRODS Build Dependency
irods-externals-mungefs1.0.2-0 - iRODS Build Dependency
irods-externals-mungefs1.0.3-0 - iRODS Build Dependency
irods-externals-nanodbc2.13.0-0 - iRODS Build Dependency
irods-externals-qpid-with-proton0.34-0 - iRODS Build Dependency
irods-externals-qpid-with-proton0.34-1 - iRODS Build Dependency
irods-externals-redis4.0.8-0 - iRODS Build Dependency
irods-externals-redis4.0.10-0 - iRODS Build Dependency
irods-externals-spdlog0.17.0-0 - iRODS Build Dependency
irods-externals-spdlog1.5.0-0 - iRODS Build Dependency
irods-externals-spdlog1.5.0-1 - iRODS Build Dependency
irods-externals-zeromq4-14.1.3-0 - iRODS Build Dependency
irods-externals-zeromq4-14.1.6-0 - iRODS Build Dependency 
irods-icommands - The integrated Rule-Oriented Data System
irods-microservice-plugins-curl - The integrated Rule-Oriented Data System
irods-resource-plugin-s3 - The integrated Rule-Oriented Data System
irods-rule-engine-plugin-apply-access-time - The integrated Rule-Oriented Data System
irods-rule-engine-plugin-audit-amqp - The integrated Rule-Oriented Data System
irods-rule-engine-plugin-data-movement - The integrated Rule-Oriented Data System
irods-rule-engine-plugin-data-replication - The integrated Rule-Oriented Data System
irods-rule-engine-plugin-data-verification - The integrated Rule-Oriented Data System
irods-rule-engine-plugin-python - The integrated Rule-Oriented Data System
irods-rule-engine-plugin-storage-tiering - The integrated Rule-Oriented Data System
irods-rule-engine-plugin-tiered-storage - The integrated Rule-Oriented Data System
irods-rule-engine-plugin-unified-storage-tiering - The integrated Rule-Oriented Data System
irods-rule-engine-plugin-update-collection-mtime - The integrated Rule-Oriented Data System
irods-runtime - The integrated Rule-Oriented Data System
irods-server - The integrated Rule-Oriented Data System
vitlacil@host:~$ 

Install iRODS iCommands

vitlacil@host:~$ sudo apt install irods-icommands 
Reading package lists... Done 
Building dependency tree       
Reading state information... Done
The following additional packages will be installed:
 irods-externals-avro1.7.7-0 irods-externals-boost1.60.0-0
 irods-externals-clang-runtime3.8-0 irods-externals-jansson2.7-0
 irods-externals-libarchive3.3.2-0 irods-externals-zeromq4-14.1.3-0
 irods-runtime python-cffi-backend python-chardet python-cryptography
 python-enum34 python-idna python-ipaddress python-ndg-httpsclient
 python-openssl python-pkg-resources python-psutil python-pyasn1
 python-requests python-six python-urllib3
Suggested packages:
 python-cryptography-doc python-cryptography-vectors python-enum34-doc
 python-openssl-doc python-openssl-dbg python-setuptools python-psutil-doc
 python-ntlm
The following NEW packages will be installed:
 irods-externals-avro1.7.7-0 irods-externals-boost1.60.0-0
 irods-externals-clang-runtime3.8-0 irods-externals-jansson2.7-0
 irods-externals-libarchive3.3.2-0 irods-externals-zeromq4-14.1.3-0
 irods-icommands irods-runtime python-cffi-backend python-chardet
 python-cryptography python-enum34 python-idna python-ipaddress
 python-ndg-httpsclient python-openssl python-pkg-resources python-psutil
 python-pyasn1 python-requests python-six python-urllib3
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Preparing to unpack .../irods-externals-jansson2.7-0_1.0~xenial_amd64.deb ...
Unpacking irods-externals-jansson2.7-0 (1.0~xenial) ...
Selecting previously unselected package irods-externals-libarchive3.3.2-0.
Preparing to unpack .../irods-externals-libarchive3.3.2-0_1.0~xenial_amd64.deb ...
Unpacking irods-externals-libarchive3.3.2-0 (1.0~xenial) ...
Selecting previously unselected package irods-externals-zeromq4-14.1.3-0.
Preparing to unpack .../irods-externals-zeromq4-14.1.3-0_1.0~xenial_amd64.deb ...
Unpacking irods-externals-zeromq4-14.1.3-0 (1.0~xenial) ...
Selecting previously unselected package irods-runtime.
Preparing to unpack .../irods-runtime_4.2.7_amd64.deb ...
Unpacking irods-runtime (4.2.7) ...
Selecting previously unselected package irods-icommands.
Preparing to unpack .../irods-icommands_4.2.7_amd64.deb ...
Unpacking irods-icommands (4.2.7) ...
Processing triggers for man-db (2.7.5-1) ...
Processing triggers for doc-base (0.10.7) ...
Processing 1 added doc-base file...
Setting up python-cffi-backend (1.5.2-1ubuntu1) ...
Setting up python-pkg-resources (20.7.0-1) ...
Setting up python-chardet (2.3.0-2) ...
Setting up python-enum34 (1.1.2-1) ...
Setting up python-idna (2.0-3) ...
Setting up python-ipaddress (1.0.16-1) ...
Setting up python-pyasn1 (0.1.9-1) ...
Setting up python-six (1.10.0-3) ...
Setting up python-cryptography (1.2.3-1ubuntu0.2) ...
Setting up python-openssl (0.15.1-2ubuntu0.2) ...
Setting up python-ndg-httpsclient (0.4.0-3) ...
Setting up python-psutil (3.4.2-1ubuntu0.1) ...
Setting up python-urllib3 (1.13.1-2ubuntu0.16.04.3) ...
Setting up python-requests (2.9.1-3ubuntu0.1) ...
Setting up irods-externals-avro1.7.7-0 (1.0~xenial) ...
Setting up irods-externals-boost1.60.0-0 (1.0~xenial) ...
Setting up irods-externals-clang-runtime3.8-0 (1.0~xenial) ...
Setting up irods-externals-jansson2.7-0 (1.0~xenial) ...
Setting up irods-externals-libarchive3.3.2-0 (1.0~xenial) ...
Setting up irods-externals-zeromq4-14.1.3-0 (1.0~xenial) ...
Setting up irods-runtime (4.2.7) ...
Setting up irods-icommands (4.2.7) ...
vitlacil@host:~$ 

Configure the iRODS environment

NOTE: Create your own configuration file !!

vitlacil@host:~$ cd /home/vitlacil/
vitlacil@host:~$ mkdir .irods
vitlacil@host:~$ cat /home/vitlacil/.irods/irods_environment.json
{
 "irods_host": "irods-login.swestore.se", 
 "irods_port": 2432,
 "irods_default_resource": "pdc-gpfs",
 "irods_home": "/snic.se/home/s_dejvi",
 "irods_cwd": "/snic.se/home/s_dejvi",
 "irods_user_name": "s_dejvi",
 "irods_zone_name": "snic.se", 
 "irods_client_server_negotiation": "request_server_negotiation",
 "irods_client_server_policy": "CS_NEG_REFUSE",
 "irods_default_hash_scheme": "SHA256",
 "irods_encryption_algorithm": "AES-256-CBC",
 "irods_encryption_key_size": 32,
 "irods_encryption_num_hash_rounds": 16,
 "irods_encryption_salt_size": 8,
 "irods_match_hash_policy": "compatible",
 "irods_authentication_scheme" : "PAM"
}

Authenticate and test iRODS iCommands client

vitlacil@host:~$ iinit
Enter your current PAM password:
vitlacil@host:~$ ils
/snic.se/home/s_dejvi:
 .DS_Store
 ._.DS_Store
 SISO.Certificate.pdf
 project_role_descriptions.docx
 worst-day-fosdem-2014.pdf
 C- /snic.se/home/s_dejvi/0 TiddlyWiki
 C- /snic.se/home/s_dejvi/0 reading
 C- /snic.se/home/s_dejvi/EOSC
 C- /snic.se/home/s_dejvi/EUDAT
 C- /snic.se/home/s_dejvi/FAIR
 C- /snic.se/home/s_dejvi/FitSM
 .....
vitlacil@host:~$

Back to Swestore-iRODS Documentation