IRODS iCommands installation on CentOS 7
Revision as of 13:30, 6 May 2020 by Dejan Vitlacil (C3SE) (talk | contribs)
Back to Swestore-iRODS Documentation [[1]]
Here is an example of iRODS iCommands installation on CentOS 7, from iRODS repository.
Contents
Install the public key and add the repository
[vitlacil@localhost ~]$ sudo rpm --import https://packages.irods.org/irods-signing-key.asc [sudo] password for vitlacil: ************************* [vitlacil@localhost ~]$ wget -qO - https://packages.irods.org/renci-irods.yum.repo | sudo tee /etc/yum.repos.d/renci-irods.yum.repo [renci-irods] name=RENCI iRODS Repository baseurl=https://packages.irods.org/yum/pool/centos$releasever/$basearch enabled=1 gpgcheck=1 repo_gpgcheck=1 gpgkey=https://packages.irods.org/irods-signing-key.asc [vitlacil@localhost ~]$
List available packages
[vitlacil@localhost ~]$ sudo yum search irods Loaded plugins: fastestmirror, langpacks Loading mirror speeds from cached hostfile * base: mirror.hosthink.net * extras: mirror.hosthink.net * updates: mirror.hosthink.net renci-irods/7/x86_64/signature | 819 B 00:00:00 Retrieving key from https://packages.irods.org/irods-signing-key.asc Importing GPG key 0xACF9B42B: Userid : "iRODS Consortium <info@irods.org>" Fingerprint: 9014 ff9f 75c6 6c77 1f1c b574 bd92 5dbd acf9 b42b From : https://packages.irods.org/irods-signing-key.asc Is this ok [y/N]: y renci-irods/7/x86_64/signature | 2.9 kB 00:00:04 !!! renci-irods/7/x86_64/primary_db | 63 kB 00:00:01 ======================================== N/S matched: irods ======================================== irods-externals-autoconf5ad3567c-0.x86_64 : iRODS Build Dependency irods-externals-avro1.7.7-0.x86_64 : iRODS Build Dependency irods-externals-avro1.8.2-0.x86_64 : iRODS Build Dependency irods-externals-avro1.9.0-0.x86_64 : iRODS Build Dependency irods-externals-aws-sdk-cpp1.4.89-0.x86_64 : iRODS Build Dependency irods-externals-aws-sdk-cpp1.4.89-1.x86_64 : iRODS Build Dependency irods-externals-boost1.60.0-0.x86_64 : iRODS Build Dependency irods-externals-boost1.67.0-0.x86_64 : iRODS Build Dependency irods-externals-catch22.3.0-0.x86_64 : iRODS Build Dependency irods-externals-clang-runtime3.8-0.x86_64 : iRODS Build Dependency irods-externals-clang-runtime6.0-0.x86_64 : iRODS Build Dependency irods-externals-clang3.8-0.x86_64 : iRODS Build Dependency irods-externals-clang6.0-0.x86_64 : iRODS Build Dependency irods-externals-cmake3.11.4-0.x86_64 : iRODS Build Dependency irods-externals-cmake3.5.2-0.x86_64 : iRODS Build Dependency irods-externals-cppzmq4.1-0.x86_64 : iRODS Build Dependency irods-externals-cppzmq4.2.3-0.x86_64 : iRODS Build Dependency irods-externals-cpr1.3.0-0.x86_64 : iRODS Build Dependency irods-externals-cpr1.3.0-1.x86_64 : iRODS Build Dependency irods-externals-elasticlient0.1.0-0.x86_64 : iRODS Build Dependency irods-externals-elasticlient0.1.0-1.x86_64 : iRODS Build Dependency irods-externals-epm4.2-0.x86_64 : iRODS Build Dependency irods-externals-fmt6.1.2-0.x86_64 : iRODS Build Dependency irods-externals-fmt6.1.2-1.x86_64 : iRODS Build Dependency irods-externals-imagemagick7.0.3-0.x86_64 : iRODS Build Dependency irods-externals-imagemagick7.0.8-0.x86_64 : iRODS Build Dependency irods-externals-jansson2.7-0.x86_64 : iRODS Build Dependency irods-externals-json3.0.1-0.x86_64 : iRODS Build Dependency irods-externals-json3.1.2-0.x86_64 : iRODS Build Dependency irods-externals-json3.7.3-0.x86_64 : iRODS Build Dependency irods-externals-libarchive3.1.2-0.x86_64 : iRODS Build Dependency irods-externals-libarchive3.3.2-0.x86_64 : iRODS Build Dependency irods-externals-libarchive3.3.2-1.x86_64 : iRODS Build Dependency irods-externals-libs359b62371-0.x86_64 : iRODS Build Dependency irods-externals-libs3a30e55e8-0.x86_64 : iRODS Build Dependency irods-externals-libs3a30e55e8-1.x86_64 : iRODS Build Dependency irods-externals-libs3f6a2098e-0.x86_64 : iRODS Build Dependency irods-externals-mungefs1.0.2-0.x86_64 : iRODS Build Dependency irods-externals-mungefs1.0.3-0.x86_64 : iRODS Build Dependency irods-externals-nanodbc2.13.0-0.x86_64 : iRODS Build Dependency irods-externals-qpid-with-proton0.34-0.x86_64 : iRODS Build Dependency irods-externals-qpid-with-proton0.34-1.x86_64 : iRODS Build Dependency irods-externals-redis4.0.10-0.x86_64 : iRODS Build Dependency irods-externals-redis4.0.8-0.x86_64 : iRODS Build Dependency irods-externals-spdlog0.17.0-0.x86_64 : iRODS Build Dependency irods-externals-spdlog1.5.0-0.x86_64 : iRODS Build Dependency irods-externals-spdlog1.5.0-1.x86_64 : iRODS Build Dependency irods-externals-zeromq4-14.1.3-0.x86_64 : iRODS Build Dependency irods-externals-zeromq4-14.1.6-0.x86_64 : iRODS Build Dependency irods-auth-plugin-gsi.x86_64 : The integrated Rule-Oriented Data System irods-auth-plugin-krb.x86_64 : The integrated Rule-Oriented Data System irods-database-plugin-mysql.x86_64 : The integrated Rule-Oriented Data System irods-database-plugin-oracle.x86_64 : The integrated Rule-Oriented Data System irods-database-plugin-postgres.x86_64 : The integrated Rule-Oriented Data System irods-devel.x86_64 : The integrated Rule-Oriented Data System irods-icommands.x86_64 : The integrated Rule-Oriented Data System irods-microservice-plugins-curl.x86_64 : The integrated Rule-Oriented Data System irods-resource-plugin-s3.x86_64 : The integrated Rule-Oriented Data System irods-rule-engine-plugin-apply-access-time.x86_64 : The integrated Rule-Oriented Data System irods-rule-engine-plugin-audit-amqp.x86_64 : The integrated Rule-Oriented Data System irods-rule-engine-plugin-data-movement.x86_64 : The integrated Rule-Oriented Data System irods-rule-engine-plugin-data-replication.x86_64 : The integrated Rule-Oriented Data System irods-rule-engine-plugin-data-verification.x86_64 : The integrated Rule-Oriented Data System irods-rule-engine-plugin-python.x86_64 : The integrated Rule-Oriented Data System irods-rule-engine-plugin-storage-tiering.x86_64 : The integrated Rule-Oriented Data System irods-rule-engine-plugin-tiered-storage.x86_64 : The integrated Rule-Oriented Data System irods-rule-engine-plugin-unified-storage-tiering.x86_64 : The integrated Rule-Oriented Data System irods-rule-engine-plugin-update-collection-mtime.x86_64 : The integrated Rule-Oriented Data System irods-runtime.x86_64 : The integrated Rule-Oriented Data System irods-server.x86_64 : The integrated Rule-Oriented Data System irods_rule_engine_plugin-apply_access_time.x86_64 : The integrated Rule-Oriented Data System irods_rule_engine_plugin-data_movement.x86_64 : The integrated Rule-Oriented Data System irods_rule_engine_plugin-data_replication.x86_64 : The integrated Rule-Oriented Data System irods_rule_engine_plugin-data_verification.x86_64 : The integrated Rule-Oriented Data System irods_rule_engine_plugin-storage_tiering.x86_64 : The integrated Rule-Oriented Data System irods_rule_engine_plugin-unified_storage_tiering.x86_64 : The integrated Rule-Oriented Data System Name and summary matches only, use "search all" for everything. [vitlacil@localhost ~]$
Install additional repositories needed for Python dependencies
[vitlacil@localhost ~]$ sudo yum install epel-release Loaded plugins: fastestmirror, langpacks Loading mirror speeds from cached hostfile * base: mirror.hosthink.net * extras: mirror.hosthink.net * updates: mirror.hosthink.net Resolving Dependencies --> Running transaction check ---> Package epel-release.noarch 0:7-11 will be installed --> Finished Dependency Resolution Dependencies Resolved ==================================================================================================== Package Arch Version Repository Size ==================================================================================================== Installing: epel-release noarch 7-11 extras 15 k Transaction Summary ==================================================================================================== Install 1 Package Total download size: 15 k Installed size: 24 k Is this ok [y/d/N]: y Downloading packages: epel-release-7-11.noarch.rpm | 15 kB 00:00:00 Running transaction check Running transaction test Transaction test succeeded Running transaction Installing : epel-release-7-11.noarch 1/1 Verifying : epel-release-7-11.noarch 1/1 Installed: epel-release.noarch 0:7-11 Complete!
... and Python dependencies
[vitlacil@localhost ~]$ sudo yum install python-psutil python-jsonschema Loaded plugins: fastestmirror, langpacks Loading mirror speeds from cached hostfile epel/x86_64/metalink | 24 kB 00:00:00 * base: mirror.zetup.net * epel: mirror.zetup.net * extras: mirror.zetup.net * updates: mirror.zetup.net epel | 4.7 kB 00:00:00 (1/3): epel/x86_64/group_gz | 95 kB 00:00:00 (2/3): epel/x86_64/updateinfo | 1.0 MB 00:00:00 (3/3): epel/x86_64/primary_db | 6.8 MB 00:00:00 Resolving Dependencies --> Running transaction check ---> Package python2-jsonschema.noarch 0:2.5.1-4.el7 will be installed --> Processing Dependency: python-repoze-lru for package: python2-jsonschema-2.5.1-4.el7.noarch ---> Package python2-psutil.x86_64 0:5.6.7-1.el7 will be installed --> Running transaction check ---> Package python-repoze-lru.noarch 0:0.4-3.el7 will be installed --> Finished Dependency Resolution Dependencies Resolved ==================================================================================================== Package Arch Version Repository Size ==================================================================================================== Installing: python2-jsonschema noarch 2.5.1-4.el7 epel 75 k python2-psutil x86_64 5.6.7-1.el7 epel 399 k Installing for dependencies: python-repoze-lru noarch 0.4-3.el7 epel 13 k Transaction Summary ==================================================================================================== Install 2 Packages (+1 Dependent package) Total download size: 487 k Installed size: 2.6 M Is this ok [y/d/N]: y Downloading packages: warning: /var/cache/yum/x86_64/7/epel/packages/python-repoze-lru-0.4-3.el7.noarch.rpm: Header V3 RSA/SHA256 Signature, key ID 352c64e5: NOKEY Public key for python-repoze-lru-0.4-3.el7.noarch.rpm is not installed (1/3): python-repoze-lru-0.4-3.el7.noarch.rpm | 13 kB 00:00:00 (2/3): python2-jsonschema-2.5.1-4.el7.noarch.rpm | 75 kB 00:00:00 (3/3): python2-psutil-5.6.7-1.el7.x86_64.rpm | 399 kB 00:00:00 ---------------------------------------------------------------------------------------------------- Total 1.3 MB/s | 487 kB 00:00:00 Retrieving key from file:///etc/pki/rpm-gpg/RPM-GPG-KEY-EPEL-7 Importing GPG key 0x352C64E5: Userid : "Fedora EPEL (7) <epel@fedoraproject.org>" Fingerprint: 91e9 7d7c 4a5e 96f1 7f3e 888f 6a2f aea2 352c 64e5 Package : epel-release-7-11.noarch (@extras) From : /etc/pki/rpm-gpg/RPM-GPG-KEY-EPEL-7 Is this ok [y/N]: y Running transaction check Running transaction test Transaction test succeeded Running transaction Installing : python-repoze-lru-0.4-3.el7.noarch 1/3 Installing : python2-jsonschema-2.5.1-4.el7.noarch 2/3 Installing : python2-psutil-5.6.7-1.el7.x86_64 3/3 Verifying : python2-jsonschema-2.5.1-4.el7.noarch 1/3 Verifying : python2-psutil-5.6.7-1.el7.x86_64 2/3 Verifying : python-repoze-lru-0.4-3.el7.noarch 3/3 Installed: python2-jsonschema.noarch 0:2.5.1-4.el7 python2-psutil.x86_64 0:5.6.7-1.el7 Dependency Installed: python-repoze-lru.noarch 0:0.4-3.el7 Complete! [vitlacil@localhost ~]$
Install iRODS iCommands
[vitlacil@localhost ~]$ sudo yum install irods-icommands Loaded plugins: fastestmirror, langpacks Loading mirror speeds from cached hostfile * base: mirrors.glesys.net * epel: mirrors.glesys.net * extras: mirrors.glesys.net * updates: mirrors.glesys.net Resolving Dependencies --> Running transaction check ---> Package irods-icommands.x86_64 0:4.2.7-1 will be installed --> Processing Dependency: irods-runtime = 4.2.7 for package: irods-icommands-4.2.7-1.x86_64 --> Processing Dependency: irods-externals-avro1.7.7-0 for package: irods-icommands-4.2.7-1.x86_64 --> Processing Dependency: irods-externals-jansson2.7-0 for package: irods-icommands-4.2.7-1.x86_64 --> Processing Dependency: irods-externals-clang-runtime3.8-0 for package: irods-icommands-4.2.7-1.x86_64 --> Processing Dependency: irods-externals-zeromq4-14.1.3-0 for package: irods-icommands-4.2.7-1.x86_64 --> Processing Dependency: irods-externals-boost1.60.0-0 for package: irods-icommands-4.2.7-1.x86_64 --> Processing Dependency: irods-externals-libarchive3.3.2-0 for package: irods-icommands-4.2.7-1.x86_64 --> Running transaction check ---> Package irods-externals-avro1.7.7-0.x86_64 0:1.0-1 will be installed ---> Package irods-externals-boost1.60.0-0.x86_64 0:1.0-1 will be installed ---> Package irods-externals-clang-runtime3.8-0.x86_64 0:1.0-1 will be installed ---> Package irods-externals-jansson2.7-0.x86_64 0:1.0-1 will be installed ---> Package irods-externals-libarchive3.3.2-0.x86_64 0:1.0-1 will be installed ---> Package irods-externals-zeromq4-14.1.3-0.x86_64 0:1.0-1 will be installed ---> Package irods-runtime.x86_64 0:4.2.7-1 will be installed --> Finished Dependency Resolution Dependencies Resolved ==================================================================================================== Package Arch Version Repository Size ==================================================================================================== Installing: irods-icommands x86_64 4.2.7-1 renci-irods 526 k Installing for dependencies: irods-externals-avro1.7.7-0 x86_64 1.0-1 renci-irods 1.5 M irods-externals-boost1.60.0-0 x86_64 1.0-1 renci-irods 13 M irods-externals-clang-runtime3.8-0 x86_64 1.0-1 renci-irods 347 k irods-externals-jansson2.7-0 x86_64 1.0-1 renci-irods 165 k irods-externals-libarchive3.3.2-0 x86_64 1.0-1 renci-irods 1.7 M irods-externals-zeromq4-14.1.3-0 x86_64 1.0-1 renci-irods 549 k irods-runtime x86_64 4.2.7-1 renci-irods 3.6 M Transaction Summary ==================================================================================================== Install 1 Package (+7 Dependent packages) Total download size: 21 M Installed size: 158 M Is this ok [y/d/N]: y Downloading packages: (1/8): irods-externals-avro1.7.7-0-1.0-1.x86_64.rpm | 1.5 MB 00:00:03 (2/8): irods-externals-clang-runtime3.8-0-1.0-1.x86_64.rpm | 347 kB 00:00:00 (3/8): irods-externals-jansson2.7-0-1.0-1.x86_64.rpm | 165 kB 00:00:00 (4/8): irods-externals-libarchive3.3.2-0-1.0-1.x86_64.rpm | 1.7 MB 00:00:03 (5/8): irods-externals-zeromq4-14.1.3-0-1.0-1.x86_64.rpm | 549 kB 00:00:01 (6/8): irods-icommands-4.2.7-1.x86_64.rpm | 526 kB 00:00:01 (7/8): irods-externals-boost1.60.0-0-1.0-1.x86_64.rpm | 13 MB 00:00:16 (8/8): irods-runtime-4.2.7-1.x86_64.rpm | 3.6 MB 00:00:08 ---------------------------------------------------------------------------------------------------- Total 1.0 MB/s | 21 MB 00:00:20 Running transaction check Running transaction test Transaction test succeeded Running transaction Installing : irods-externals-avro1.7.7-0-1.0-1.x86_64 1/8 Installing : irods-externals-boost1.60.0-0-1.0-1.x86_64 2/8 Installing : irods-externals-zeromq4-14.1.3-0-1.0-1.x86_64 3/8 Installing : irods-externals-libarchive3.3.2-0-1.0-1.x86_64 4/8 Installing : irods-externals-jansson2.7-0-1.0-1.x86_64 5/8 Installing : irods-externals-clang-runtime3.8-0-1.0-1.x86_64 6/8 Installing : irods-runtime-4.2.7-1.x86_64 7/8 Installing : irods-icommands-4.2.7-1.x86_64 8/8 Verifying : irods-externals-clang-runtime3.8-0-1.0-1.x86_64 1/8 Verifying : irods-externals-jansson2.7-0-1.0-1.x86_64 2/8 Verifying : irods-externals-libarchive3.3.2-0-1.0-1.x86_64 3/8 Verifying : irods-externals-zeromq4-14.1.3-0-1.0-1.x86_64 4/8 Verifying : irods-externals-boost1.60.0-0-1.0-1.x86_64 5/8 Verifying : irods-icommands-4.2.7-1.x86_64 6/8 Verifying : irods-externals-avro1.7.7-0-1.0-1.x86_64 7/8 Verifying : irods-runtime-4.2.7-1.x86_64 8/8 Installed: irods-icommands.x86_64 0:4.2.7-1 Dependency Installed: irods-externals-avro1.7.7-0.x86_64 0:1.0-1 irods-externals-boost1.60.0-0.x86_64 0:1.0-1 irods-externals-clang-runtime3.8-0.x86_64 0:1.0-1 irods-externals-jansson2.7-0.x86_64 0:1.0-1 irods-externals-libarchive3.3.2-0.x86_64 0:1.0-1 irods-externals-zeromq4-14.1.3-0.x86_64 0:1.0-1 irods-runtime.x86_64 0:4.2.7-1 Complete! [vitlacil@localhost ~]$
Configure the iRODS environment
NOTE: Create your own configuration file !!
[vitlacil@localhost ~]$ 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@localhost ~]$
Authenticate and test iRODS iCommands client
[vitlacil@localhost ~]$ iinit Enter your current PAM password: ************************* [vitlacil@localhost ~]$ 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@localhost ~]$
