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We present DarkFlux, a software tool designed to analyze indirect-detection signatures for next-generation models of dark matter (DM) with multiple annihilation channels. Version 1.0 of this tool accepts user-generated models with $2\to 2$ tree-level dark matter annihilation to pairs of Standard Model (SM) particles and analyzes DM annihilation to $γ$ rays. The tool consists of three modules -- the annihilation fraction module, the flux module, and the analysis module -- which can be run in a loop in order to scan over DM mass if desired. [A description of each module is available in the full abstract.] DarkFlux v1.0 compares the total $γ$-ray flux to a joint-likelihood analysis of fifteen dwarf spheroidal galaxies (dSphs) analyzed by the $Fermi$-LAT collaboration. DarkFlux automatically provides data tables and can plot the output of the three modules. In this manual, we briefly motivate this indirect-detection computer tool and review the essential DM physics. We then describe the several modules of DarkFlux in greater detail. Finally, we show how to install and run DarkFlux and provide two worked examples demonstrating its capabilities.