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# REMADE — REMADE Estimates (Meta)genomic Ancient Damage Efficiently     --- #### Work in progress. Please contact christianmichelsen@gmail.com for further information. --- Personal recommendations for this project: <!-- - Python Version: [Pyenv](https://github.com/pyenv/pyenv) --> <!-- - Virtual Environment: [Virtualenv](https://github.com/pyenv/pyenv-virtualenv) --> - Package management and virtual environment: [Poetry](https://python-poetry.org/) This project requires a recent Python version (>=3.8) installed. See more [below](#setup). ## <a name="install"></a> Installation: With Poetry: ```console $ poetry add remade ``` or, if you prefer regular pip: ```console $ pip install remade ``` ## <a name="dependencies"></a> Dependencies: `remade` depends on having ngslca (metadamage) installed somewhere on your system. Personally, I have it installed here: `/Users/christianmichelsen/work/thorfinn_metaLCA/metadamage`. ## <a name="cli"></a> REMADE CLI: For help on the CLI interface, `remade` provides a `help` function: ```console $ remade --help ``` Example for fitting a single file using `remade`: ```console $ remade compute raw_data/subs.original.bam \ --names raw_data/names.dmp.gz \ --nodes raw_data/nodes.dmp.gz \ --acc2tax raw_data/combined_taxid_accssionNO_20200425.gz \ --ngslca-command /Users/christianmichelsen/work/thorfinn_metaLCA/metadamage ``` ## <a name="dash"></a> Dashboard: To make use of the new, interactive dashboard introduced in version `0.4`, run the following command (after having [computed](#cli) the fit results): ```console $ remade dashboard ``` And then open a browser and go to `127.0.0.1:8050` (if it did not open automatically). For more information, use: ```console $ remade dashboard --help ``` ## <a name="dash-server"></a> Dashboard on a server: If you are running remade on a server and want to use the dashboard locally, you can setup a SSH tunnel. First, on the server, run `remade dashboard` with the relevant options (and keep it open, e.g. with [TMUX](https://github.com/tmux/tmux/wiki)). Afterwards, on your local machine, run: ```console $ ssh -L 8050:127.0.0.1:8050 -N user@remote ``` Now you can open a browser and go to [`http://0.0.0.0:8050`](http://0.0.0.0:8050). In case you're connecting through a jump host, you can use the the `-J` option: ```console $ ssh -L 8050:127.0.0.1:8050 -N -J user@jumphost user@remote ``` For an easier method, you can setup your ssh config (usually at `~/.ssh/config`) in the following way: ```ssh-config Host jumphost User your-jumphost-username-here HostName your-jumphost-address-here Host remote Host dashboard Port 22 LocalForward 8050 localhost:8050 RemoteCommand echo "Connecting to dashboard ... CTRL+C to terminate"; sleep infinity Host remote dashboard ProxyJump jumphost User your-remote-username-here HostName your-remote-address-here ``` Now if you simply run the following on your own computer (in a new terminal session): ```console $ ssh dashboard ``` you can open open a browser and go to [`http://0.0.0.0:8050`](http://0.0.0.0:8050). <!-- ssh -L 8050:127.0.0.1:8050 -N -J willerslev mnv794@wonton-snm --> <!-- ssh -L 8050:127.0.0.1:8050 -N -J mnv794@ssh-snm-willerslev.science.ku.dk mnv794@wonton-snm --> <!-- ssh -L 8050:127.0.0.1:8050 -N hep --> ## <a name="options"></a> remade compute CLI options: The `remade compute` CLI first takes `bam_files` as an argument. This argument is either a single (or multiple) bam-files or a directory containing bam-file(s). In addition, `remade compute` also takes the following options. - Input files: - `--names`: Path to the (NCBI) `names.dmp.gz`. - `--nodes`: Path to the (NCBI) `nodes.dmp.gz`. - `--acc2tax`: Path to the (NCBI) `acc2tax.gz`. - ngsLCA parameters: - `--ngsLCA-command`: The command needed to run the ngsLCA-program. - `--simscorelow`: Number between 0-1. - `--simscorehigh`: Number between 0-1. - `--minmapq`: Minimum mapping quality. - `--howmany`: Maximum position in the sequence to include. Default is +/- 15 (forward/reverse). - `--lca-rank`: The LCA rank used in ngsLCA. Can be either `family`, `genus`, or `species`. Default is `species`. - General parameters: - `--storage_path`: Path where the generated output files and folders are stored. - `--max-cores`: The maximum number of cores to use in the ancient damage estimation. - Boolean flags (does not take any values, only the flag). Default is false. - `--bayesian`: Include a fully Bayesian model (probably better, but also _a lot_ slower, about a factor of 100). - `--forced`: Ignore previously generated results. - Other: - `--help`: Print the help documentation and exit. - `--version`: Print the current version of the program and exit. <!-- [tex-image-link-generator](https://tex-image-link-generator.herokuapp.com/) --> <!-- https://gist.github.com/a-rodin/fef3f543412d6e1ec5b6cf55bf197d7b --> --- ## <a name="setup"></a> Setup Local Python Environment: Make sure you have a decent Python version (>=3.8) installed. Personally, I recommend using Poetry to manage your virtual environments. We now use Poetry to setup a new project which uses remade: ```console $ poetry new remade-poetry $ cd remade-poetry ``` We now have a working local, virtual Python environment where the packages are managed by Poetry, so we can now add metadamamage to our project: ```console $ poetry add remade ``` <!-- poetry config --list --> <!-- poetry config virtualenvs.in-project true --> <!-- poetry shell --> <!-- source $(poetry env info --path)/bin/activate --> <!-- git clone https://github.com/ChristianMichelsen/remade.git remade-git --> <!-- poetry install --> At this point you should log out of your terminal and log in again for reloading everything. Now if you just write: ```console $ remade --help ``` you should see the following: ```console $ remade compute Usage: remade [OPTIONS] COMMAND [ARGS]... REMADE — REMADE Estimates (Meta)genomic Ancient Damage Efficiently. ... ``` which shows that it is working and installed. --- ## <a name="update"></a> Update: With Poetry: ```console $ poetry update remade ``` or, if you prefer regular pip: ```console $ pip install remade --upgrade ``` --- ## <a name="dev_branch"></a> Development Branch: You can also use a newer version directly from Github: ```console $ poetry add git+https://github.com/ChristianMichelsen/remade.git ``` or a specific branch (named `BRANCH`): ```console $ poetry add git+https://github.com/ChristianMichelsen/remade.git#BRANCH ``` --- ## Conda: If you prefer using Conda, you can also install `remade` (via pip). First create a folder: ```console $ mkdir remade-conda $ cd remade-conda ``` To install `remade`: ```console $ wget https://raw.githubusercontent.com/ChristianMichelsen/remade/main/environment.yaml $ conda env create -f environment.yaml ``` To update it to a new, released version of `remade`: ```console $ wget https://raw.githubusercontent.com/ChristianMichelsen/remade/main/environment.yaml $ conda env update --file environment.yaml ``` Finally remember to activate the environment: ```console $ conda activate remade ``` <!-- poetry add git+https://github.com/christianmichelsen/remade.git --> <!-- poetry add git+https://github.com/christianmichelsen/remade.git#develop --> <!-- git clone https://github.com/ChristianMichelsen/REMADE.git remade-git -->