{"action":"created","issue":{"url":"https://api.github.com/repos/Vaa3D/v3d_external/issues/6","repository_url":"https://api.github.com/repos/Vaa3D/v3d_external","labels_url":"https://api.github.com/repos/Vaa3D/v3d_external/issues/6/labels{/name}","comments_url":"https://api.github.com/repos/Vaa3D/v3d_external/issues/6/comments","events_url":"https://api.github.com/repos/Vaa3D/v3d_external/issues/6/events","html_url":"https://github.com/Vaa3D/v3d_external/issues/6","id":185306382,"number":6,"title":"vaa3d failed to call plugin on CentOS server due to X server","user":{"login":"lsqshr","id":1567877,"avatar_url":"https://avatars.githubusercontent.com/u/1567877?v=3","gravatar_id":"","url":"https://api.github.com/users/lsqshr","html_url":"https://github.com/lsqshr","followers_url":"https://api.github.com/users/lsqshr/followers","following_url":"https://api.github.com/users/lsqshr/following{/other_user}","gists_url":"https://api.github.com/users/lsqshr/gists{/gist_id}","starred_url":"https://api.github.com/users/lsqshr/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lsqshr/subscriptions","organizations_url":"https://api.github.com/users/lsqshr/orgs","repos_url":"https://api.github.com/users/lsqshr/repos","events_url":"https://api.github.com/users/lsqshr/events{/privacy}","received_events_url":"https://api.github.com/users/lsqshr/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/Vaa3D/v3d_external/labels/help%20wanted","name":"help wanted","color":"159818"}],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":9,"created_at":"2016-10-26T06:18:15Z","updated_at":"2016-10-27T15:35:43Z","closed_at":null,"body":"With the 3.200 CentOS release, I tried to start plugins on a CentOS server without X server. Vaa3D complains `cannot connect to X server` for all plugins.\r\n\r\nI can reproduce this error with simply `vaa3d -h`\r\n```\r\nVaa3D: a 3D image visualization and analysis platform developed by Hanchuan Peng and colleagues.\r\n\r\nUsage: v3d -h -M moduleCode [all other options specific to different modules]\r\n    -h/H         help information.\r\n    -i <file>                    open single or multiple image (.tif/.tiff, .lsm, .mrc, .raw/.v3draw) / object (.ano, .apo, .swc, .marker) files\r\n    -o <file>                    indicates single or multiple outputs\r\n    -x <plugin_dll_full_path or unique partial path>    a string indicates the full path or a unique partial path of a dll (for a plugin) to be launched.\r\n    -m <menu_name>               a string indicates which menu of a plugin will be called.\r\n    -f <function_name>           a string indicates which function of a plugin will be called.\r\n    -p <parameters>              a string indicates parameters that plugin function use\r\n    -pf <configuration>          a string read from configuration file indicates parameters that plugin function use\r\n    -v                           force to open a 3d viewer when loading an image, otherwise use the default v3d global setting (from \"Adjust Preference\")\r\n    -na                          open NeuronAnnotator work-mode directly\r\n    -cmd  [headless command-line arguments, intended for compute grid use. Try '-cmd -h' for more information on this option]\r\n: cannot connect to X server\r\n```\r\n\r\nI can evoke plugins from command line on my local ubuntu without trouble.\r\n\r\nIs it a known issue?"},"comment":{"url":"https://api.github.com/repos/Vaa3D/v3d_external/issues/comments/256677795","html_url":"https://github.com/Vaa3D/v3d_external/issues/6#issuecomment-256677795","issue_url":"https://api.github.com/repos/Vaa3D/v3d_external/issues/6","id":256677795,"user":{"login":"zhizhoualan","id":11778162,"avatar_url":"https://avatars.githubusercontent.com/u/11778162?v=3","gravatar_id":"","url":"https://api.github.com/users/zhizhoualan","html_url":"https://github.com/zhizhoualan","followers_url":"https://api.github.com/users/zhizhoualan/followers","following_url":"https://api.github.com/users/zhizhoualan/following{/other_user}","gists_url":"https://api.github.com/users/zhizhoualan/gists{/gist_id}","starred_url":"https://api.github.com/users/zhizhoualan/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/zhizhoualan/subscriptions","organizations_url":"https://api.github.com/users/zhizhoualan/orgs","repos_url":"https://api.github.com/users/zhizhoualan/repos","events_url":"https://api.github.com/users/zhizhoualan/events{/privacy}","received_events_url":"https://api.github.com/users/zhizhoualan/received_events","type":"User","site_admin":false},"created_at":"2016-10-27T15:35:43Z","updated_at":"2016-10-27T15:35:43Z","body":"Thanks for your suggestion! I will give it a try!\n\nOn Wed, Oct 26, 2016 at 10:07 PM, Siqi Liu <notifications@github.com> wrote:\n\n> Another thing is about the start_vaa3d.sh on Linux machines. I start v3d\n> several times a day on ubuntu and the script was pretty painful. What about\n> including a one shot setup script for Linux machines?\n>\n> The one I am using for Ubuntu\n>\n> #setup_vaa3d.sh#!/bin/sh\n> dname=$(dirname $(realpath $0));\n> # Remove the old ones made by Vaa3D\n> sed -i '/^export V3DPATH=/d' ~/.bashrc;\n> sed -i '/^alias v3d=/d' ~/.bashrc;\n> sed -i '/export LD_LIBRARY_PATH=.*Vaa3D_Ubuntu_.*/d' ~/.bashrc;\n> # Add new Vaa3D shortcutsecho \"export V3DPATH=\\\"$dname\\\";\" >> ~/.bashrc; # Append the current path to PATHecho \"export LD_LIBRARY_PATH=\\$LD_LIBRARY_PATH:$dname;\" >> ~/.bashrc;echo \"alias v3d=\\\"$dname/vaa3d\\\";\" >> ~/.bashrc; # Make alias for v3d\n>\n> For centos it should be\n>\n> #setup_vaa3d.sh#!/bin/sh\n> dname=$(dirname $(realpath $0));\n> # Remove the old ones made by Vaa3D\n> sed -i '/^export V3DPATH=/d' ~/.bashrc;\n> sed -i '/^alias v3d=/d' ~/.bashrc;\n> sed -i '/export LD_LIBRARY_PATH=.*Vaa3D_Ubuntu_.*/d' ~/.bashrc;\n> # Add new Vaa3D shortcutsecho \"export V3DPATH=\\\"$dname\\\";\" >> ~/.bashrc; # Append the current path to PATHecho \"export LD_LIBRARY_PATH=\\$LD_LIBRARY_PATH:$dname;\" >> ~/.bashrc;echo \"alias v3d=\\\"export DISPLAY=:30;Xvfb :30 -auth /dev/null & $dname/vaa3d\\\";\" >> ~/.bashrc; # Make alias for v3d\n>\n> In this way, your terminal does not have to go to the vaa3d folder to\n> start v3d.\n>\n> —\n> You are receiving this because you were mentioned.\n> Reply to this email directly, view it on GitHub\n> <https://github.com/Vaa3D/v3d_external/issues/6#issuecomment-256547626>,\n> or mute the thread\n> <https://github.com/notifications/unsubscribe-auth/ALO4cq5TOY1EuAchHEEJnek3kmE4jOFaks5q4DGMgaJpZM4KgzG2>\n> .\n>\n"}}
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