IRODS iCommands installation on Ubuntu 20.04

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Install the public key and add the repository

Prepare IRODS APT repository (#Using bionic repos because focal is not available) 

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:~$

List available packages

dejan@dejan:~$ apt-cache search irods
python3-irodsclient - Client API for iRods
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-avro1.8.2-0 - 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-boost1.67.0-0 - iRODS Build Dependency
irods-externals-catch22.3.0-0 - iRODS Build Dependency
irods-externals-clang6.0-0 - iRODS Build Dependency
irods-externals-clang-runtime6.0-0 - iRODS Build Dependency
irods-externals-cmake3.11.4-0 - 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-elasticlient0.1.0-1 - iRODS Build Dependency
irods-externals-fmt6.1.2-1 - iRODS Build Dependency
irods-externals-imagemagick7.0.8-0 - iRODS Build Dependency
irods-externals-jansson2.7-0 - iRODS Build Dependency
irods-externals-json3.1.2-0 - iRODS Build Dependency
irods-externals-json3.7.3-0 - iRODS Build Dependency
irods-externals-libarchive3.3.2-1 - iRODS Build Dependency
irods-externals-libs3a30e55e8-1 - iRODS Build Dependency
irods-externals-libs34e684077-0 - iRODS Build Dependency
irods-externals-libs359b62371-0 - 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-proton0.34-1 - iRODS Build Dependency
irods-externals-qpid-with-proton0.34-2 - 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-zeromq4-14.1.6-0 - 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-audit-amqp - The integrated Rule-Oriented Data System
irods-rule-engine-plugin-document-type - The integrated Rule-Oriented Data System
irods-rule-engine-plugin-elasticsearch - The integrated Rule-Oriented Data System
irods-rule-engine-plugin-hard-links - The integrated Rule-Oriented Data System
irods-rule-engine-plugin-indexing - The integrated Rule-Oriented Data System
irods-rule-engine-plugin-logical-quotas - The integrated Rule-Oriented Data System
irods-rule-engine-plugin-metadata-guard - The integrated Rule-Oriented Data System
irods-rule-engine-plugin-python - 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
dejan@dejan:~$


Install python-urlib3, python-requests and libssl1.0.0

  • Short version:
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-1ubuntu5.6_amd64.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-1ubuntu5.6_amd64.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-1ubuntu5.6_amd64.deb
  • Long version:
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-1ubuntu5.6_amd64.deb
--2021-03-16 18:13:02--  http://security.ubuntu.com/ubuntu/pool/main/p/python-urllib3/python-urllib3_1.22-1ubuntu0.18.04.2_all.deb
Resolving security.ubuntu.com (security.ubuntu.com)... 91.189.88.142, 91.189.88.152, 91.189.91.38, ...
Connecting to security.ubuntu.com (security.ubuntu.com)|91.189.88.142|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 86024 (84K) [application/x-debian-package]
Saving to: ‘python-urllib3_1.22-1ubuntu0.18.04.2_all.deb’

python-urllib3_1.22-1ubuntu0.18.04.2_al 100%[===============================================================================>]  84.01K  --.-KB/s    in 0.06s    

2021-03-16 18:13:02 (1.39 MB/s) - ‘python-urllib3_1.22-1ubuntu0.18.04.2_all.deb’ saved [86024/86024]

--2021-03-16 18:13:02--  http://security.ubuntu.com/ubuntu/pool/main/r/requests/python-requests_2.18.4-2ubuntu0.1_all.deb
Reusing existing connection to security.ubuntu.com:80.
HTTP request sent, awaiting response... 200 OK
Length: 58496 (57K) [application/x-debian-package]
Saving to: ‘python-requests_2.18.4-2ubuntu0.1_all.deb’

python-requests_2.18.4-2ubuntu0.1_all.d 100%[===============================================================================>]  57.12K  --.-KB/s    in 0.01s   

2021-03-16 18:13:02 (3.94 MB/s) - ‘python-requests_2.18.4-2ubuntu0.1_all.deb’ saved [58496/58496]

--2021-03-16 18:13:02--  http://security.ubuntu.com/ubuntu/pool/main/o/openssl1.0/libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb
Reusing existing connection to security.ubuntu.com:80.
HTTP request sent, awaiting response... 200 OK
Length: 1088600 (1.0M) [application/x-debian-package]
Saving to: ‘libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb’

libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb 100%[===============================================================================>]   1.04M  --.-KB/s    in 0.09s   

2021-03-16 18:13:02 (11.1 MB/s) - ‘libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb’ saved [1088600/1088600]

FINISHED --2021-03-16 18:13:02--
Total wall clock time: 0.4s
Downloaded: 3 files, 1.2M in 0.2s (7.08 MB/s)
dejan@dejan:~$ 

dejan@dejan:~$ 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-1ubuntu5.6_amd64.deb
Reading package lists... Done
Building dependency tree       
Reading state information... Done
Note, selecting 'python-urllib3' instead of './python-urllib3_1.22-1ubuntu0.18.04.2_all.deb'
Note, selecting 'python-requests' instead of './python-requests_2.18.4-2ubuntu0.1_all.deb'
Note, selecting 'libssl1.0.0' instead of './libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb'
The following additional packages will be installed:
  libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib python-certifi python-cffi-backend python-chardet python-cryptography python-enum34 python-idna
  python-ipaddress python-is-python2 python-openssl python-pkg-resources python-six python2 python2-minimal python2.7 python2.7-minimal
Suggested packages:
  python-cryptography-doc python-cryptography-vectors python-enum34-doc python-openssl-doc python-openssl-dbg python-setuptools python-socks python-ntlm
  python2-doc python-tk python2.7-doc binutils binfmt-support
The following NEW packages will be installed:
  libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib libssl1.0.0 python-certifi python-cffi-backend python-chardet python-cryptography python-enum34
  python-idna python-ipaddress python-is-python2 python-openssl python-pkg-resources python-requests python-six python-urllib3 python2 python2-minimal
  python2.7 python2.7-minimal
0 upgraded, 21 newly installed, 0 to remove and 23 not upgraded.
Need to get 4,644 kB/5,877 kB of archives.
After this operation, 25.0 MB of additional disk space will be used.
Do you want to continue? [Y/n] y
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Get:2 /home/dejan/python-urllib3_1.22-1ubuntu0.18.04.2_all.deb python-urllib3 all 1.22-1ubuntu0.18.04.2 [86.0 kB]
Get:3 /home/dejan/python-requests_2.18.4-2ubuntu0.1_all.deb python-requests all 2.18.4-2ubuntu0.1 [58.5 kB]
Get:4 http://se.archive.ubuntu.com/ubuntu focal-updates/universe amd64 libpython2.7-minimal amd64 2.7.18-1~20.04.1 [335 kB]
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Get:11 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-certifi all 2019.11.28-1 [149 kB]
Get:12 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-cffi-backend amd64 1.14.0-1build1 [69.6 kB]
Get:13 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-pkg-resources all 44.0.0-2 [129 kB]
Get:14 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-chardet all 3.0.4-4build1 [80.5 kB]
Get:15 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-enum34 all 1.1.6-2ubuntu1 [34.9 kB]
Get:16 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-ipaddress all 1.0.17-1build1 [18.4 kB]
Get:17 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-six all 1.14.0-2 [12.0 kB]
Get:18 http://se.archive.ubuntu.com/ubuntu focal-updates/universe amd64 python-cryptography amd64 2.8-3ubuntu0.1 [254 kB]
Get:19 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-idna all 2.8-1 [34.5 kB]
Get:20 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-is-python2 all 2.7.17-4 [2,496 B]
Get:21 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-openssl all 19.0.0-1build1 [43.1 kB]
Fetched 4,644 kB in 0s (19.2 MB/s)    
Preconfiguring packages ...
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(Reading database ... 71260 files and directories currently installed.) 
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Setting up libpython2.7-minimal:amd64 (2.7.18-1~20.04.1) ...
Setting up python2.7-minimal (2.7.18-1~20.04.1) ...
Linking and byte-compiling packages for runtime python2.7...
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Setting up libssl1.0.0:amd64 (1.0.2n-1ubuntu5.6) ...
Setting up libpython2.7-stdlib:amd64 (2.7.18-1~20.04.1) ...
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Setting up python-idna (2.8-1) ...
Setting up python-ipaddress (1.0.17-1build1) ...
Setting up python-is-python2 (2.7.17-4) ...
Setting up python-cffi-backend (1.14.0-1build1) ...
Setting up python-enum34 (1.1.6-2ubuntu1) ...
Setting up python-urllib3 (1.22-1ubuntu0.18.04.2) ...
Setting up python-pkg-resources (44.0.0-2) ...
Setting up python-cryptography (2.8-3ubuntu0.1) ...
Setting up python-chardet (3.0.4-4build1) ...
Setting up python-requests (2.18.4-2ubuntu0.1) ...
Setting up python-openssl (19.0.0-1build1) ...
Processing triggers for libc-bin (2.31-0ubuntu9.2) ...
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dejan@dejan:~$

Install iRODS iCommands

dejan@dejan:~$ sudo apt install -y irods-icommands
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-catch22.3.0-0 irods-externals-clang-runtime6.0-0 irods-externals-fmt6.1.2-1
  irods-externals-json3.7.3-0 irods-externals-libarchive3.3.2-1 irods-externals-nanodbc2.13.0-0 irods-externals-zeromq4-14.1.6-0 irods-runtime python-psutil
Suggested packages:
  python-psutil-doc
The following NEW packages will be installed:
  irods-externals-avro1.9.0-0 irods-externals-boost1.67.0-0 irods-externals-catch22.3.0-0 irods-externals-clang-runtime6.0-0 irods-externals-fmt6.1.2-1
  irods-externals-json3.7.3-0 irods-externals-libarchive3.3.2-1 irods-externals-nanodbc2.13.0-0 irods-externals-zeromq4-14.1.6-0 irods-icommands irods-runtime
  python-psutil
0 upgraded, 12 newly installed, 0 to remove and 23 not upgraded.
Need to get 31.0 MB of archives.
After this operation, 228 MB of additional disk space will be used.
Get:1 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-psutil amd64 5.5.1-1ubuntu4 [141 kB]
Get:2 https://packages.irods.org/apt bionic/main amd64 irods-externals-avro1.9.0-0 amd64 1.0~bionic [1,886 kB]
Get:3 https://packages.irods.org/apt bionic/main amd64 irods-externals-boost1.67.0-0 amd64 1.0~bionic [17.0 MB]
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Processing triggers for man-db (2.9.1-1) ...
dejan@dejan:~$

Configure the iRODS environment

dejan@dejan:~$ 
dejan@dejan:~$ cat /home/dejan/.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"
}
dejan@dejan:~$

Authenticate and test iRODS iCommands client

dejan@dejan:~$ iinit
Enter your current PAM password:
dejan@dejan:~$ 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
.....
dejan@dejan:~$