{"action":"opened","issue":{"url":"https://api.github.com/repos/galaxyproject/tools-devteam/issues/362","repository_url":"https://api.github.com/repos/galaxyproject/tools-devteam","labels_url":"https://api.github.com/repos/galaxyproject/tools-devteam/issues/362/labels{/name}","comments_url":"https://api.github.com/repos/galaxyproject/tools-devteam/issues/362/comments","events_url":"https://api.github.com/repos/galaxyproject/tools-devteam/issues/362/events","html_url":"https://github.com/galaxyproject/tools-devteam/issues/362","id":144901568,"number":362,"title":"How to access a genome fasta index (FAI) build with data_manager_sam_fasta_index_builder (qustion also on biostars)","user":{"login":"chrausch","id":15678929,"avatar_url":"https://avatars.githubusercontent.com/u/15678929?v=3","gravatar_id":"","url":"https://api.github.com/users/chrausch","html_url":"https://github.com/chrausch","followers_url":"https://api.github.com/users/chrausch/followers","following_url":"https://api.github.com/users/chrausch/following{/other_user}","gists_url":"https://api.github.com/users/chrausch/gists{/gist_id}","starred_url":"https://api.github.com/users/chrausch/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/chrausch/subscriptions","organizations_url":"https://api.github.com/users/chrausch/orgs","repos_url":"https://api.github.com/users/chrausch/repos","events_url":"https://api.github.com/users/chrausch/events{/privacy}","received_events_url":"https://api.github.com/users/chrausch/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2016-03-31T13:29:15Z","updated_at":"2016-03-31T13:29:15Z","closed_at":null,"body":"I am modifying a galaxy tool (in testtoolshed: falco) that should have access to samtools fasta indices of reference genomes.\r\n\r\nCurrently, in the tool's xml file: REF_FILE=\"${genomeSource.indices.fields.path}\" is called.\r\n\r\nBut this links to /home/galaxy/galaxy/tool-data/hg19/seq in case hg19 is selected. I rather want it to look in: /home/galaxy/galaxy/tool-data/hg19/sam_indexes/hg19\r\n\r\nWhat are the galaxy-internal variables to build up the path to this location?\r\n\r\nThanks, Christian\r\n"}}