... | ... | @@ -45,8 +45,8 @@ If the SeqScreen conda/container is not used, there are additional programs and |
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| Taxonomic Identification | Outlier Detection* | `s2fast_changes` git branch | MIT License | https://github.com/marbl/ATLAS/tree/s2fast_changes | none* |
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| Taxonomic Identification | DIAMOND | 2.0.14 | GPLv3 | https://github.com/bbuchfink/diamond/releases/download/v2.0.14/diamond-linux64.tar.gz | `tar -xvzf diamond-linux64.tar.gz -C {installDir}/software` |
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| Taxonomic Identification | Centrifuge | 1.0.4_beta | GPLv3 | https://github.com/DaehwanKimLab/centrifuge/archive/v1.0.4-beta.tar.gz | `tar -xvzf v1.0.4-beta.tar.gz -C {installDir}/software` then `cd centrifuge-1.0.4-beta` and `make` and `sudo make install prefix=/usr/local` |
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| Taxonomic Identification | MMSeqs2 | 13.45111 | GPLv3 | https://mmseqs.com/latest/mmseqs-linux-avx2.tar.gz, https://mmseqs.com/latest/mmseqs-osx-universal.tar.gz | `tar xzf https://mmseqs.com/latest/mmseqs-(linux-avx2, osx-universal).tar.gz; export PATH=$(pwd)/mmseqs/bin/:$PATH` |
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| Functional Annotation | MUMmer** | 3.23 | Artistic License 2.0 | https://sourceforge.net/projects/mummer/files/mummer/3.23/MUMmer3.23.tar.gz | first run `tar -xvzf mummer-3.23.tar.gz -C {installDir}/software` then run `cd {installDir}/software/mummer-3.23/ && ./configure && make`|
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| Taxonomic Identification (ONT) | Minimap2 | 2.24 | MIT | https://github.com/lh3/minimap2/releases/download/v2.24/minimap2-2.24_x64-linux.tar.bz2 | `curl -L https://github.com/lh3/minimap2/releases/download/v2.24/minimap2-2.24_x64-linux.tar.bz2 \| tar -jxvf - ./minimap2-2.24_x64-linux/minimap2`
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*The BLAST outlier detection capability does not need to be installed separately, but for informational purposes, more details about it can be found here: https://github.com/marbl/ATLAS. The BLAST outlier detection module does require SciPy to be installed via Python version 3.7, which is available in Miniconda3. To check if you already have this module available, first type: `python` to bring up Python interactive interpreter (please check that this brings up Python version 3.7). Then, type `import scipy`. If the console returns `ModuleNotFoundError`, then SciPy is not yet installed. Conversely, if the console does not return anything (just continuing allowing entry to the interpreter), then the module has been installed. To install SciPy, first exit the interactive interpreter model by typing `exit()`. Then type `python -m pip install --user scipy`.
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