IRODS iCommands installation on Ubuntu 16.04

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Revision as of 20:45, 6 May 2020 by Dejan Vitlacil (C3SE) (talk | contribs) (Created page with " == 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 vitla...")
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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:~$

vitlacil@host:~$ vitlacil@host:~$ vitlacil@host:~$ vitlacil@host:~$ vitlacil@host:~$ vitlacil@host:~$ vitlacil@host:~$ vitlacil@host:~$ 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) ... Selecting previously unselected package python-pyasn1. Preparing to unpack .../python-pyasn1_0.1.9-1_all.deb ... Unpacking python-pyasn1 (0.1.9-1) ... Selecting previously unselected package python-six. Preparing to unpack .../python-six_1.10.0-3_all.deb ... Unpacking python-six (1.10.0-3) ... Selecting previously unselected package python-cryptography. Preparing to unpack .../python-cryptography_1.2.3-1ubuntu0.2_amd64.deb ... Unpacking python-cryptography (1.2.3-1ubuntu0.2) ... Selecting previously unselected package python-openssl. Preparing to unpack .../python-openssl_0.15.1-2ubuntu0.2_all.deb ... Unpacking python-openssl (0.15.1-2ubuntu0.2) ... Selecting previously unselected package python-ndg-httpsclient. Preparing to unpack .../python-ndg-httpsclient_0.4.0-3_all.deb ... Unpacking python-ndg-httpsclient (0.4.0-3) ... Selecting previously unselected package python-psutil. Preparing to unpack .../python-psutil_3.4.2-1ubuntu0.1_amd64.deb ... Unpacking python-psutil (3.4.2-1ubuntu0.1) ... Selecting previously unselected package python-urllib3. Preparing to unpack .../python-urllib3_1.13.1-2ubuntu0.16.04.3_all.deb ... Unpacking python-urllib3 (1.13.1-2ubuntu0.16.04.3) ... Selecting previously unselected package python-requests. Preparing to unpack .../python-requests_2.9.1-3ubuntu0.1_all.deb ... Unpacking python-requests (2.9.1-3ubuntu0.1) ... Selecting previously unselected package irods-externals-avro1.7.7-0. Preparing to unpack .../irods-externals-avro1.7.7-0_1.0~xenial_amd64.deb ... Unpacking irods-externals-avro1.7.7-0 (1.0~xenial) ... Selecting previously unselected package irods-externals-boost1.60.0-0. Preparing to unpack .../irods-externals-boost1.60.0-0_1.0~xenial_amd64.deb ... Unpacking irods-externals-boost1.60.0-0 (1.0~xenial) ... Selecting previously unselected package irods-externals-clang-runtime3.8-0. Preparing to unpack .../irods-externals-clang-runtime3.8-0_1.0~xenial_amd64.deb ... 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:~$ vitlacil@host:~$ vitlacil@host:~$ vitlacil@host:~$ vitlacil@host:~$ vitlacil@host:~$ vitlacil@host:~$ vitlacil@host:~$ vitlacil@host:~$ ienv 

ERROR: environment_properties::capture: missing environment file. should be at [/home/vitlacil/.irods/irods_environment.json]

irods_version - 4.2.7 vitlacil@host:~$ touch /home/vitlacil/.irods/irods_environment.json 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. After this operation, 30,0 MB of additional disk space will be used. Do you want to continue? [Y/n] y Get:2 http://se.archive.ubuntu.com/ubuntu xenial-updates/main amd64 vim amd64 2:7.4.1689-3ubuntu1.4 [1 036 kB] 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] Fetched 6 205 kB in 0s (12,6 MB/s) Selecting previously unselected package vim-runtime. (Reading database ... 225701 files and directories currently installed.) Preparing to unpack .../vim-runtime_2%3a7.4.1689-3ubuntu1.4_all.deb ... Adding 'diversion of /usr/share/vim/vim74/doc/help.txt to /usr/share/vim/vim74/doc/help.txt.vim-tiny by vim-runtime' Adding 'diversion of /usr/share/vim/vim74/doc/tags to /usr/share/vim/vim74/doc/tags.vim-tiny by vim-runtime' Unpacking vim-runtime (2:7.4.1689-3ubuntu1.4) ... Selecting previously unselected package vim. Preparing to unpack .../vim_2%3a7.4.1689-3ubuntu1.4_amd64.deb ... Unpacking vim (2:7.4.1689-3ubuntu1.4) ... 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
 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/Dropbox
 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/FAIR
 C- /snic.se/home/s_dejvi/FitSM
 C- /snic.se/home/s_dejvi/Googletakeout
 C- /snic.se/home/s_dejvi/Magazines
 C- /snic.se/home/s_dejvi/PIDs
 C- /snic.se/home/s_dejvi/Private
 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:~$

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