IRODS iCommands installation on Ubuntu 16.04
Revision as of 20:57, 6 May 2020 by Dejan Vitlacil (C3SE) (talk | contribs) (→Install the public key and add the repository)
Back to Swestore-iRODS Documentation
Contents
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 Get:4 http://security.ubuntu.com/ubuntu xenial-security InRelease [109 kB] 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 0 upgraded, 22 newly installed, 0 to remove and 0 not upgraded. Need to get 25,9 MB of archives. After this operation, 199 MB of additional disk space will be used. Do you want to continue? [Y/n] y Get:1 http://se.archive.ubuntu.com/ubuntu xenial/main amd64 python-cffi-backend amd64 1.5.2-1ubuntu1 [58,1 kB] Get:2 http://se.archive.ubuntu.com/ubuntu xenial/main amd64 python-pkg-resources all 20.7.0-1 [108 kB] Get:3 http://se.archive.ubuntu.com/ubuntu xenial/main amd64 python-chardet all 2.3.0-2 [96,3 kB] Get:4 http://se.archive.ubuntu.com/ubuntu xenial/main amd64 python-enum34 all 1.1.2-1 [35,8 kB] Get:5 http://se.archive.ubuntu.com/ubuntu xenial/main amd64 python-idna all 2.0-3 [35,1 kB] Get:6 http://se.archive.ubuntu.com/ubuntu xenial/main amd64 python-ipaddress all 1.0.16-1 [18,0 kB] Get:7 http://se.archive.ubuntu.com/ubuntu xenial/main amd64 python-pyasn1 all 0.1.9-1 [45,1 kB] Get:8 http://se.archive.ubuntu.com/ubuntu xenial/main amd64 python-six all 1.10.0-3 [10,9 kB] Get:9 http://se.archive.ubuntu.com/ubuntu xenial-updates/main amd64 python-cryptography amd64 1.2.3-1ubuntu0.2 [199 kB] Get:10 http://se.archive.ubuntu.com/ubuntu xenial-updates/main amd64 python-openssl all 0.15.1-2ubuntu0.2 [84,9 kB] Get:11 http://se.archive.ubuntu.com/ubuntu xenial/main amd64 python-ndg-httpsclient all 0.4.0-3 [25,1 kB] Get:12 http://se.archive.ubuntu.com/ubuntu xenial-updates/main amd64 python-psutil amd64 3.4.2-1ubuntu0.1 [55,4 kB] Get:13 http://se.archive.ubuntu.com/ubuntu xenial-updates/main amd64 python-urllib3 all 1.13.1-2ubuntu0.16.04.3 [58,4 kB] Get:14 http://se.archive.ubuntu.com/ubuntu xenial-updates/main amd64 python-requests all 2.9.1-3ubuntu0.1 [55,9 kB] Get:15 https://packages.irods.org/apt xenial/main amd64 irods-externals-avro1.7.7-0 amd64 1.0~xenial [1 566 kB] Get:16 https://packages.irods.org/apt xenial/main amd64 irods-externals-boost1.60.0-0 amd64 1.0~xenial [13,8 MB] Get:17 https://packages.irods.org/apt xenial/main amd64 irods-externals-clang-runtime3.8-0 amd64 1.0~xenial [374 kB] Get:18 https://packages.irods.org/apt xenial/main amd64 irods-externals-jansson2.7-0 amd64 1.0~xenial [162 kB] Get:19 https://packages.irods.org/apt xenial/main amd64 irods-externals-libarchive3.3.2-0 amd64 1.0~xenial [1 732 kB] Get:20 https://packages.irods.org/apt xenial/main amd64 irods-externals-zeromq4-14.1.3-0 amd64 1.0~xenial [568 kB] Get:21 https://packages.irods.org/apt xenial/main amd64 irods-runtime amd64 4.2.7 [5 854 kB] Get:22 https://packages.irods.org/apt xenial/main amd64 irods-icommands amd64 4.2.7 [989 kB] Fetched 25,9 MB in 17s (1 476 kB/s) Selecting previously unselected package python-cffi-backend. (Reading database ... 212721 files and directories currently installed.) Preparing to unpack .../python-cffi-backend_1.5.2-1ubuntu1_amd64.deb ... Unpacking python-cffi-backend (1.5.2-1ubuntu1) ... Selecting previously unselected package python-pkg-resources. Preparing to unpack .../python-pkg-resources_20.7.0-1_all.deb ... Unpacking python-pkg-resources (20.7.0-1) ... Selecting previously unselected package python-chardet. Preparing to unpack .../python-chardet_2.3.0-2_all.deb ... Unpacking python-chardet (2.3.0-2) ... Selecting previously unselected package python-enum34. Preparing to unpack .../python-enum34_1.1.2-1_all.deb ... Unpacking python-enum34 (1.1.2-1) ... Selecting previously unselected package python-idna. Preparing to unpack .../python-idna_2.0-3_all.deb ... Unpacking python-idna (2.0-3) ... Selecting previously unselected package python-ipaddress. Preparing to unpack .../python-ipaddress_1.0.16-1_all.deb ... Unpacking python-ipaddress (1.0.16-1) ... 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Unpacking irods-externals-clang-runtime3.8-0 (1.0~xenial) ... Selecting previously unselected package irods-externals-jansson2.7-0. 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:~$
