IRODS iCommands installation on CentOS 7

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Revision as of 13:03, 6 May 2020 by Dejan Vitlacil (C3SE) (talk | contribs) (Authenticate and test iRODS iCommands client)
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Here is an example of iRODS iCommands installation on CentOS 7, from iRODS repository.

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

[vitlacil@localhost ~]$ vi /home/vitlacil/.irods/irods_environment.json

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 ~]$