{"action":"created","comment":{"url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/pulls/comments/78685840","id":78685840,"diff_hunk":"@@ -72,18 +72,24 @@ Root authority is required for these steps.\n ## 3. access from remote client\n \n 1. start RDP client (ex. Windows remote desktop) in remote client.\n- \n+\n 2. specify \"\\<IP address of host OS\\>:5017\" as the destination to access.<br>\n    Of course, you can change the port. Please see Readme.txt in cisCall vbox tarball.\n-  \n+\n 3. login with user=\"cisusr\", password=\"cisusrcisusr\".\n    The cisCall modules and all prerequisit files are set under /home/cisusr/cisCall.\n-               \n+\n 4. run cisCall with prepared small examples.<br>\n   - cisFusion: execute `$ ./example.fusion.sh` at /home/cisusr/run_cisFuion.\n   - cisMuton: execute `$ ./example.muton.sh` at /home/cisusr/run_cisMuton.\n   - cisCton: execute `$ ./example.cton.sh` at /home/cisusr/run_cisCton.\n \n+Note:\n+    Since cisCton utilizes a same bam file generated by running cisMuton, it requires\n+    bam file which has been output by running cisMuton.\n+    Namely `/path/to/working/directory/output/${sample_name}/common.fastq.aln.bam`.","path":"doc/INSTALL.md","position":31,"original_position":31,"commit_id":"ed2fa113ce71612ea964ae29811a6df98ddb8516","original_commit_id":"ed2fa113ce71612ea964ae29811a6df98ddb8516","user":{"login":"joemphilips","id":10084960,"avatar_url":"https://avatars.githubusercontent.com/u/10084960?v=3","gravatar_id":"","url":"https://api.github.com/users/joemphilips","html_url":"https://github.com/joemphilips","followers_url":"https://api.github.com/users/joemphilips/followers","following_url":"https://api.github.com/users/joemphilips/following{/other_user}","gists_url":"https://api.github.com/users/joemphilips/gists{/gist_id}","starred_url":"https://api.github.com/users/joemphilips/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/joemphilips/subscriptions","organizations_url":"https://api.github.com/users/joemphilips/orgs","repos_url":"https://api.github.com/users/joemphilips/repos","events_url":"https://api.github.com/users/joemphilips/events{/privacy}","received_events_url":"https://api.github.com/users/joemphilips/received_events","type":"User","site_admin":false},"body":"> fastqも、Prerequisite filesに入れたほうが良いのでは?(今頃すみません)\r\nで、その延長でctonが必要とするbamも。これは、詳細はcton.mdを見ろ、でいいと思いますが。。。\r\n\r\nかしこまりました。追記します。","created_at":"2016-09-14T04:50:07Z","updated_at":"2016-09-14T04:50:07Z","html_url":"https://github.com/NCCJapan/cisCall5_doc/pull/6#discussion_r78685840","pull_request_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/pulls/6","_links":{"self":{"href":"https://api.github.com/repos/NCCJapan/cisCall5_doc/pulls/comments/78685840"},"html":{"href":"https://github.com/NCCJapan/cisCall5_doc/pull/6#discussion_r78685840"},"pull_request":{"href":"https://api.github.com/repos/NCCJapan/cisCall5_doc/pulls/6"}}},"pull_request":{"url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/pulls/6","id":85165084,"html_url":"https://github.com/NCCJapan/cisCall5_doc/pull/6","diff_url":"https://github.com/NCCJapan/cisCall5_doc/pull/6.diff","patch_url":"https://github.com/NCCJapan/cisCall5_doc/pull/6.patch","issue_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/issues/6","number":6,"state":"open","locked":false,"title":"explain why Muton has been run before Cton","user":{"login":"joemphilips","id":10084960,"avatar_url":"https://avatars.githubusercontent.com/u/10084960?v=3","gravatar_id":"","url":"https://api.github.com/users/joemphilips","html_url":"https://github.com/joemphilips","followers_url":"https://api.github.com/users/joemphilips/followers","following_url":"https://api.github.com/users/joemphilips/following{/other_user}","gists_url":"https://api.github.com/users/joemphilips/gists{/gist_id}","starred_url":"https://api.github.com/users/joemphilips/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/joemphilips/subscriptions","organizations_url":"https://api.github.com/users/joemphilips/orgs","repos_url":"https://api.github.com/users/joemphilips/repos","events_url":"https://api.github.com/users/joemphilips/events{/privacy}","received_events_url":"https://api.github.com/users/joemphilips/received_events","type":"User","site_admin":false},"body":"「Ctonを走らせる前にMutonを動かしてbamを準備すること」といった旨の説明を追記しました。","created_at":"2016-09-14T04:26:25Z","updated_at":"2016-09-14T04:50:07Z","closed_at":null,"merged_at":null,"merge_commit_sha":"194d154a4dcab266896b9ed53fc867f78b124e5d","assignee":{"login":"monagai","id":13533333,"avatar_url":"https://avatars.githubusercontent.com/u/13533333?v=3","gravatar_id":"","url":"https://api.github.com/users/monagai","html_url":"https://github.com/monagai","followers_url":"https://api.github.com/users/monagai/followers","following_url":"https://api.github.com/users/monagai/following{/other_user}","gists_url":"https://api.github.com/users/monagai/gists{/gist_id}","starred_url":"https://api.github.com/users/monagai/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/monagai/subscriptions","organizations_url":"https://api.github.com/users/monagai/orgs","repos_url":"https://api.github.com/users/monagai/repos","events_url":"https://api.github.com/users/monagai/events{/privacy}","received_events_url":"https://api.github.com/users/monagai/received_events","type":"User","site_admin":false},"assignees":[{"login":"monagai","id":13533333,"avatar_url":"https://avatars.githubusercontent.com/u/13533333?v=3","gravatar_id":"","url":"https://api.github.com/users/monagai","html_url":"https://github.com/monagai","followers_url":"https://api.github.com/users/monagai/followers","following_url":"https://api.github.com/users/monagai/following{/other_user}","gists_url":"https://api.github.com/users/monagai/gists{/gist_id}","starred_url":"https://api.github.com/users/monagai/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/monagai/subscriptions","organizations_url":"https://api.github.com/users/monagai/orgs","repos_url":"https://api.github.com/users/monagai/repos","events_url":"https://api.github.com/users/monagai/events{/privacy}","received_events_url":"https://api.github.com/users/monagai/received_events","type":"User","site_admin":false}],"milestone":null,"commits_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/pulls/6/commits","review_comments_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/pulls/6/comments","review_comment_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/pulls/comments{/number}","comments_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/issues/6/comments","statuses_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/statuses/ed2fa113ce71612ea964ae29811a6df98ddb8516","head":{"label":"NCCJapan:update_cton_explanation","ref":"update_cton_explanation","sha":"ed2fa113ce71612ea964ae29811a6df98ddb8516","user":{"login":"NCCJapan","id":13513984,"avatar_url":"https://avatars.githubusercontent.com/u/13513984?v=3","gravatar_id":"","url":"https://api.github.com/users/NCCJapan","html_url":"https://github.com/NCCJapan","followers_url":"https://api.github.com/users/NCCJapan/followers","following_url":"https://api.github.com/users/NCCJapan/following{/other_user}","gists_url":"https://api.github.com/users/NCCJapan/gists{/gist_id}","starred_url":"https://api.github.com/users/NCCJapan/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/NCCJapan/subscriptions","organizations_url":"https://api.github.com/users/NCCJapan/orgs","repos_url":"https://api.github.com/users/NCCJapan/repos","events_url":"https://api.github.com/users/NCCJapan/events{/privacy}","received_events_url":"https://api.github.com/users/NCCJapan/received_events","type":"Organization","site_admin":false},"repo":{"id":66815704,"name":"cisCall5_doc","full_name":"NCCJapan/cisCall5_doc","owner":{"login":"NCCJapan","id":13513984,"avatar_url":"https://avatars.githubusercontent.com/u/13513984?v=3","gravatar_id":"","url":"https://api.github.com/users/NCCJapan","html_url":"https://github.com/NCCJapan","followers_url":"https://api.github.com/users/NCCJapan/followers","following_url":"https://api.github.com/users/NCCJapan/following{/other_user}","gists_url":"https://api.github.com/users/NCCJapan/gists{/gist_id}","starred_url":"https://api.github.com/users/NCCJapan/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/NCCJapan/subscriptions","organizations_url":"https://api.github.com/users/NCCJapan/orgs","repos_url":"https://api.github.com/users/NCCJapan/repos","events_url":"https://api.github.com/users/NCCJapan/events{/privacy}","received_events_url":"https://api.github.com/users/NCCJapan/received_events","type":"Organization","site_admin":false},"private":false,"html_url":"https://github.com/NCCJapan/cisCall5_doc","description":"repository for hosting html document for cisCall5","fork":false,"url":"https://api.github.com/repos/NCCJapan/cisCall5_doc","forks_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/forks","keys_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/keys{/key_id}","collaborators_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/teams","hooks_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/hooks","issue_events_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/issues/events{/number}","events_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/events","assignees_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/assignees{/user}","branches_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/branches{/branch}","tags_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/tags","blobs_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/git/refs{/sha}","trees_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/git/trees{/sha}","statuses_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/statuses/{sha}","languages_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/languages","stargazers_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/stargazers","contributors_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/contributors","subscribers_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/subscribers","subscription_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/subscription","commits_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/commits{/sha}","git_commits_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/git/commits{/sha}","comments_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/comments{/number}","issue_comment_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/issues/comments{/number}","contents_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/contents/{+path}","compare_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/compare/{base}...{head}","merges_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/merges","archive_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/{archive_format}{/ref}","downloads_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/downloads","issues_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/issues{/number}","pulls_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/pulls{/number}","milestones_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/milestones{/number}","notifications_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/notifications{?since,all,participating}","labels_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/labels{/name}","releases_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/releases{/id}","deployments_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/deployments","created_at":"2016-08-29T06:00:21Z","updated_at":"2016-09-05T12:58:57Z","pushed_at":"2016-09-14T04:26:25Z","git_url":"git://github.com/NCCJapan/cisCall5_doc.git","ssh_url":"git@github.com:NCCJapan/cisCall5_doc.git","clone_url":"https://github.com/NCCJapan/cisCall5_doc.git","svn_url":"https://github.com/NCCJapan/cisCall5_doc","homepage":null,"size":630,"stargazers_count":0,"watchers_count":0,"language":"Shell","has_issues":true,"has_downloads":true,"has_wiki":true,"has_pages":true,"forks_count":1,"mirror_url":null,"open_issues_count":3,"forks":1,"open_issues":3,"watchers":0,"default_branch":"master"}},"base":{"label":"NCCJapan:master","ref":"master","sha":"23c258d5eca3256c69766957efb9b89c0aa0198c","user":{"login":"NCCJapan","id":13513984,"avatar_url":"https://avatars.githubusercontent.com/u/13513984?v=3","gravatar_id":"","url":"https://api.github.com/users/NCCJapan","html_url":"https://github.com/NCCJapan","followers_url":"https://api.github.com/users/NCCJapan/followers","following_url":"https://api.github.com/users/NCCJapan/following{/other_user}","gists_url":"https://api.github.com/users/NCCJapan/gists{/gist_id}","starred_url":"https://api.github.com/users/NCCJapan/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/NCCJapan/subscriptions","organizations_url":"https://api.github.com/users/NCCJapan/orgs","repos_url":"https://api.github.com/users/NCCJapan/repos","events_url":"https://api.github.com/users/NCCJapan/events{/privacy}","received_events_url":"https://api.github.com/users/NCCJapan/received_events","type":"Organization","site_admin":false},"repo":{"id":66815704,"name":"cisCall5_doc","full_name":"NCCJapan/cisCall5_doc","owner":{"login":"NCCJapan","id":13513984,"avatar_url":"https://avatars.githubusercontent.com/u/13513984?v=3","gravatar_id":"","url":"https://api.github.com/users/NCCJapan","html_url":"https://github.com/NCCJapan","followers_url":"https://api.github.com/users/NCCJapan/followers","following_url":"https://api.github.com/users/NCCJapan/following{/other_user}","gists_url":"https://api.github.com/users/NCCJapan/gists{/gist_id}","starred_url":"https://api.github.com/users/NCCJapan/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/NCCJapan/subscriptions","organizations_url":"https://api.github.com/users/NCCJapan/orgs","repos_url":"https://api.github.com/users/NCCJapan/repos","events_url":"https://api.github.com/users/NCCJapan/events{/privacy}","received_events_url":"https://api.github.com/users/NCCJapan/received_events","type":"Organization","site_admin":false},"private":false,"html_url":"https://github.com/NCCJapan/cisCall5_doc","description":"repository for hosting html document for cisCall5","fork":false,"url":"https://api.github.com/repos/NCCJapan/cisCall5_doc","forks_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/forks","keys_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/keys{/key_id}","collaborators_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/teams","hooks_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/hooks","issue_events_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/issues/events{/number}","events_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/events","assignees_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/assignees{/user}","branches_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/branches{/branch}","tags_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/tags","blobs_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/git/refs{/sha}","trees_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/git/trees{/sha}","statuses_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/statuses/{sha}","languages_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/languages","stargazers_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/stargazers","contributors_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/contributors","subscribers_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/subscribers","subscription_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/subscription","commits_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/commits{/sha}","git_commits_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/git/commits{/sha}","comments_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/comments{/number}","issue_comment_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/issues/comments{/number}","contents_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/contents/{+path}","compare_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/compare/{base}...{head}","merges_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/merges","archive_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/{archive_format}{/ref}","downloads_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/downloads","issues_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/issues{/number}","pulls_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/pulls{/number}","milestones_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/milestones{/number}","notifications_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/notifications{?since,all,participating}","labels_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/labels{/name}","releases_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/releases{/id}","deployments_url":"https://api.github.com/repos/NCCJapan/cisCall5_doc/deployments","created_at":"2016-08-29T06:00:21Z","updated_at":"2016-09-05T12:58:57Z","pushed_at":"2016-09-14T04:26:25Z","git_url":"git://github.com/NCCJapan/cisCall5_doc.git","ssh_url":"git@github.com:NCCJapan/cisCall5_doc.git","clone_url":"https://github.com/NCCJapan/cisCall5_doc.git","svn_url":"https://github.com/NCCJapan/cisCall5_doc","homepage":null,"size":630,"stargazers_count":0,"watchers_count":0,"language":"Shell","has_issues":true,"has_downloads":true,"has_wiki":true,"has_pages":true,"forks_count":1,"mirror_url":null,"open_issues_count":3,"forks":1,"open_issues":3,"watchers":0,"default_branch":"master"}},"_links":{"self":{"href":"https://api.github.com/repos/NCCJapan/cisCall5_doc/pulls/6"},"html":{"href":"https://github.com/NCCJapan/cisCall5_doc/pull/6"},"issue":{"href":"https://api.github.com/repos/NCCJapan/cisCall5_doc/issues/6"},"comments":{"href":"https://api.github.com/repos/NCCJapan/cisCall5_doc/issues/6/comments"},"review_comments":{"href":"https://api.github.com/repos/NCCJapan/cisCall5_doc/pulls/6/comments"},"review_comment":{"href":"https://api.github.com/repos/NCCJapan/cisCall5_doc/pulls/comments{/number}"},"commits":{"href":"https://api.github.com/repos/NCCJapan/cisCall5_doc/pulls/6/commits"},"statuses":{"href":"https://api.github.com/repos/NCCJapan/cisCall5_doc/statuses/ed2fa113ce71612ea964ae29811a6df98ddb8516"}}}}
{"actor":{"display_login":"joemphilips"}}