| use rayon::prelude::*; | |
| /// Returns the indices that would sort a vector in parallel | |
| fn par_argsort<T: Ord + Sync>(data: &[T]) -> Vec<usize> { | |
| let mut indices = (0..data.len()).collect::<Vec<_>>(); | |
| indices.par_sort_unstable_by_key(|&i| &data[i]); | |
| indices | |
| } |
| /// Reverse complement a DNA sequence with bit-twiddling | |
| /// | |
| /// # Example | |
| /// | |
| /// ```rust | |
| /// let seq = b"ATGCTTCCAGAA"; | |
| /// | |
| /// let actual = revcomp(seq); | |
| /// let expected = b"TTCTGGAAGCAT";/// | |
| /// assert_eq!(actual, expected) |
| // Future versions of Hyper may add additional config options, | |
| // which will not automatically be merged into this file. | |
| // See https://hyper.is#cfg for all currently supported options. | |
| module.exports = { | |
| config: { | |
| // choose either `'stable'` for receiving highly polished, | |
| // or `'canary'` for less polished but more frequent updates | |
| updateChannel: 'stable', |
At the moment, the best solution for running deepbinner (GPU) on the EBI cluster is using
a Singularity container and requesting a whole GPU to yourself. The reason for
needing to request a whole GPU is a horrible mess of tensorflow, cuda, memory sharing,
and my lack of proper GPU architecture understanding.
The image I have been using to run deepbinner (v0.2.0) can be pulled with
| MIT License | |
| Copyright (c) 2017 Michael Hall | |
| Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: | |
| The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. | |
| THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE O |
| .idea/ |
| .DS_Store | |
| .idea |
| MIT License | |
| Copyright (c) 2017 Michael Hall | |
| Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: | |
| The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. | |
| THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE O |