From 7a8a0cd2d763ac88cbbf98ce89fc9f167c91921a Mon Sep 17 00:00:00 2001 From: Gentaro Shigita <40628880+shigita@users.noreply.github.com> Date: Thu, 19 Dec 2024 18:44:41 +0100 Subject: [PATCH] Update docs - Unified installation instructions in `README.md` and documentation. --- README.md | 4 +- docs/content/basics/installation.md | 125 +++++++++++++--------------- 2 files changed, 60 insertions(+), 69 deletions(-) diff --git a/README.md b/README.md index 691cc7c..84d4bc3 100644 --- a/README.md +++ b/README.md @@ -25,7 +25,7 @@ conda create -n captus -c bioconda -c conda-forge captus > > ### Important for macOS users > -> One of the builds of the latest version of `MEGAHIT` (v.1.2.9) on `Bioconda` is broken. To ensure you install a functional one, please specify the build number as follows: +> One of the builds of the latest version of `MEGAHIT` (v1.2.9) on `Bioconda` is broken. To ensure you install a functional one, please specify the build number as follows: > > ```shell > conda create -n captus -c bioconda -c conda-forge captus megahit=1.2.9=hfbae3c0_0 @@ -73,7 +73,7 @@ For help on a particular command: captus_assembly command -h ### Manual installation -If you are unable to use conda/mamba for any reason, you will need to install all dependencies manually. Please refer to the [documentation](https://edgardomortiz.github.io/captus.docs/basics/installation/#manual-installation) for details. +If you are unable to use `conda`/`mamba` for any reason, you will need to install all dependencies manually. Please refer to the [documentation](https://edgardomortiz.github.io/captus.docs/basics/installation/#manual-installation) for details. ## USAGE diff --git a/docs/content/basics/installation.md b/docs/content/basics/installation.md index 93f073d..10906f2 100644 --- a/docs/content/basics/installation.md +++ b/docs/content/basics/installation.md @@ -3,41 +3,31 @@ title = "Installation" weight = 15 +++ -### *The easy way (recommended)* +### Using conda/mamba (recommended) -The simplest way to install `Captus` is to create an isolated software environment using `conda`, if you don't have `conda` we recommend to install `miniconda` from [https://docs.conda.io/en/latest/miniconda.html](https://docs.conda.io/en/latest/miniconda.html). Once you have `conda` installed in your system you need to configure your channels: -```bash -conda config --prepend channels bioconda -conda config --prepend channels conda-forge -conda config --show channels -``` +`Captus` is available as a [conda package](https://anaconda.org/bioconda/captus). If you have `conda` [](https://docs.conda.io/projects/conda/en/latest/index.html) or `mamba` [](https://mamba.readthedocs.io/en/latest/index.html) installed, you can easily create a new environment and install `Captus` with all dependencies using the following command: -The last command should show your current channels, the order matters: -```bash -channels: - - conda-forge - - bioconda - - defaults +```shell +conda create -n captus -c bioconda -c conda-forge captus ``` -Now we are ready to create a separate environment for Captus: -```bash -conda create -n captus captus -``` +{{% notice warning "Important for macOS users" %}} +One of the builds of the latest version of `MEGAHIT` (v1.2.9) on `Bioconda` is broken. To ensure you install a functional one, please specify the build number as follows: -`conda` sometimes takes too long to find and configure dependencies, if that happens we recommend installing `mamba` first, and installing `Captus` with it: -```bash -conda install mamba -mamba create -n captus captus +```console +conda create -n captus -c bioconda -c conda-forge captus megahit=1.2.9=hfbae3c0_0 ``` -Once `Captus` is installed in its own environment, let's activate it: -```console +{{% /notice %}} +Check that `Captus` was correctly installed: + +```shell conda activate captus +captus -h ``` -And that is all! Notice that the beginning of your prompt should have changed from`(base)$` to `(captus)$` as we activate the environment. -Just to verify it is correctly installed try typing `captus --help`, if everything went OK you should see the following output in the terminal: +If the program was correctly installed, you will see the following help message: + ```console usage: captus command [options] @@ -70,53 +60,54 @@ For help on a particular command: captus_assembly command -h ``` ___ -### *The manual way* - -You will have to install all the the dependencies separately yourself: - -`Captus` was written for `python >= v3.6`, the only required library is `tqdm` but if you want to produce the HTML reports you will also need `pandas` and `plotly` - -- `BBTools` (https://jgi.doe.gov/data-and-tools/bbtools/) - -- `BioPerl` (https://bioperl.org/) - -- `BLAT >= 36x7` (http://hgdownload.soe.ucsc.edu/admin/exe/) **\*** - -- `ClipKIT` (https://github.com/JLSteenwyk/ClipKIT) - -- `FastQC` (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) or `Falco` (https://github.com/smithlabcode/falco) - -- `MAFFT` (https://mafft.cbrc.jp/alignment/software/) - -- `MEGAHIT` (https://github.com/voutcn/megahit) -- `MMseqs2` (https://github.com/soedinglab/MMseqs2) - -- `MUSCLE` (https://www.drive5.com/muscle/) - -- `pigz` (https://zlib.net/pigz/) - -- `Salmon` (https://github.com/COMBINE-lab/salmon) - -- `Scipio` (https://www.webscipio.org/) **\*** - -- `VSEARCH` (https://github.com/torognes/vsearch) - -- `YAML` (https://metacpan.org/pod/YAML) - -**\*** Bundled with `Captus` - -Once you have all the dependencies installed you can proceed to clone the repository and install `Captus` as described before: - -```console +### Manual installation + +If you are unable to use `conda`/`mamba` for any reason, you will need to manually install all the dependencies listed below: + +|Dependency|Version|URL| +|-|-|-| +|`Python` |>=3.6|| +|`BBTools`||| +|`BioPerl`||| +|`ClipKIT`|>=1.3.0|| +|`Falco`|>=0.3.0|| +|`FastQC`||| +|`MAFFT`||| +|`MEGAHIT`|1.2.9|| +|`MMseqs2`||| +|`MUSCLE`|>=5.1|| +|`pandas`|>=2.1.0|| +|`Plotly`||| +|`pigz`||| +|`Salmon`|>=1.10.0|| +|`tqdm`||| +|`VSEARCH`||| +|`YAML`||| + +**\*** The following two dependencies are bundled with `Captus`, so no additional installation is required. + +|Dependency|Version|URL| +|-|-|-| +|`BLAT`|37x1|| +|`Scipio`|1.4.1|| + +Once you have all the dependencies installed, you can proceed to clone the repository and install `Captus` as follows: + +```shell git clone https://github.com/edgardomortiz/Captus.git cd Captus pip install . +captus -h +``` + +Alternatively, you can run `Captus` using the wrapper script `captus_assembly-runner.py` as follows: + +```shell +git clone https://github.com/edgardomortiz/Captus.git +./Captus/captus_assembly-runner.py -h ``` -{{% notice tip %}} -If you don't want to install `Captus` you can simply add the directory where you cloned the repository to your system `$PATH` and use `captus_assembly-runner.py` instead of `captus` -{{% /notice %}} ___ Created by [Edgardo M. Ortiz]({{< ref "../more/credits/#edgardo-m-ortiz">}}) (06.08.2021) -Last modified by [Edgardo M. Ortiz]({{< ref "../more/credits/#edgardo-m-ortiz">}}) (19.12.2024) \ No newline at end of file +Last modified by [Gentaro Shigita]({{< ref "../../more/credits/#gentaro-shigita">}}) (19.12.2024)