/
1.7.lua
30 lines (23 loc) · 1.12 KB
/
1.7.lua
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-- -*- lua -*-
-- Written by MC on 3/5/2019
help(
[[
This module sets up bioBakery container by aliasing the container shell login to the bioBakery command
Based on DockerHub container https://hub.docker.com/r/biobakery/workflows
Run as "runbioBakery arguments".
]])
depends_on("singularity")
local BBPATH="/uufs/chpc.utah.edu/sys/installdir/bioBakery/1.7"
set_shell_function("startbioBakery",'singularity shell -s /bin/bash ' .. BBPATH .. '/bioBakery.sif',"singularity shell -s /bin/bash " .. BBPATH .. "/bioBakery.sif")
set_shell_function("runbioBakery",'singularity exec ' .. BBPATH .. '/bioBakery.sif "$@"',"singularity exec " .. BBPATH .. "/bioBakery.sif $*")
-- to export the shell function to a subshell
if (myShellName() == "bash") then
execute{cmd="export -f startbioBakery",modeA={"load"}}
execute{cmd="export -f runbioBakery",modeA={"load"}}
end
whatis("Name : bioBakery")
whatis("Version : 1.7")
whatis("Category : A virtual environment for meta'omic analysis")
whatis("URL : https://bitbucket.org/biobakery/biobakery/wiki/Home")
whatis("Installed on 03/05/2019")
whatis("Installed by : Martin Cuma")