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ARGs Desktop

Setup Environment

ARGs Desktop might call some necessary softwares via inter-process protocol, so you need to install necessary depencendes and do little configure so that ARGs Desktop can find it properly.

ARGs Desktop will find the depencendes through PATH, once dependences are placed properly, you can check and configure PATH in ARGs Desktop’s interface later.

ARGs Desktop needs blast >=2.12, bwa >=0.7.17, diamond >=2.0.15, pandas, python >=3.7, samtools >=1.15, r-base <4 and R libraries rmarkdown flexdashboard ggplot2 plotly rgdal reshape2 ggnewscale gridExtra kableExtra.

Linux/MacOS

Install Dependencies

You can easily solve everything using conda.

conda create -n args_desktop -c bioconda -c conda-forge "blast>=2.12" "bwa>=0.7.17" "diamond>=2.0.15" pandas "python>=3.7" "samtools>=1.15" "r-base<4" "pkgconfig" "r-rmarkdown" "pandoc<2.19" "r-flexdashboard" "r-ggplot2" "r-plotly" "r-rgdal" "r-reshape2" "r-ggnewscale" "r-gridExtra" "r-kableExtra"
  • Tips: Solving dependencies may take very long time with default solver, you could install the conda libmamba solver plugin with conda install -n base conda-libmamba-solver, then append --experimental-solver=libmamba to the command, so you can use: 
      conda create -n args_desktop -c bioconda -c conda-forge "blast>=2.12" "bwa>=0.7.17" "diamond>=2.0.15" pandas "python>=3.7" "samtools>=1.15" "r-base<4" "pkgconfig" "r-rmarkdown" "pandoc<2.19" "r-flexdashboard" "r-ggplot2" "r-plotly" "r-rgdal" "r-reshape2" "r-ggnewscale" "r-gridExtra" "r-kableExtra" --experimental-solver=libmamba
  • For Apple Silicon(m1/m2 series) users: Please note that you should install macOS Intel x86 64-bit version conda as some dependences do not provide ARM version.

Configure ARGs Desktop

  1. Get the binary path of dependencies by running: conda activate args_desktop , echo $PATH , normally, you just need to copy the first path for use in later steps. You can also add other paths by joining them using :.
  2. Open the client and navigate to the settings page. Enter the path including the dependencies binaries you got from step 1 into the “Extra Path” textbox and click “Save”.
  3. Verify that the client can read the dependencies by navigating to the “Environment Information” page.

Windows

Manually solve dependences

Download these binaries and copy them to %APPDATA%\args-desktop\bin.

  • Tips: you can reach that directory by clicking Settings->Environment Information->Binary Directory on ARGs Desktop or opening the path in explorer.

For some dependences do not provided compiled windows releases, to save your time, we help you compile them and you can choose to use them.

blast>=2.12

Official Website Releases

diamond>=2.0.15

GitHub Releases

samtools >=1.15

self-compile samtools_1.16.1

GitHub Source Code

bwa>=0.7.17

self-compile bwa_0.7.17

GitHub Source Code

minimap2

self-compile minimap2_2.24

GitHub Source Code

* You should follow the agreements of each module.

Install R

Then, you are required to install R libraries in conda and set the corresponding PATH in the Settings->Extra Paths in the ARGs Desktop.

Install R with Conda

conda create -n args_desktop -c conda-forge "r-base<4" "pkgconfig" "r-rmarkdown" "pandoc<2.19" "r-flexdashboard" "r-ggplot2" "r-plotly" "r-rgdal" "r-reshape2" "r-ggnewscale" "r-gridExtra" "r-kableExtra"
  • Tips: Solving dependencies may take very long time with default solver, you could install the conda libmamba solver plugin with conda install -n base conda-libmamba-solver, then append --experimental-solver=libmamba to the command. 
      conda create -n args_desktop -c conda-forge "r-base<4" "pkgconfig" "r-rmarkdown" "pandoc<2.19" "r-flexdashboard" "r-ggplot2" "r-plotly" "r-rgdal" "r-reshape2" "r-ggnewscale" "r-gridExtra" "r-kableExtra" --experimental-solver=libmamba

Configure ARGs Desktop

  1. Get the binary path of dependencies by running: conda activate args_desktop, then run PATH, normally, you just need to copy the paths including args_desktop. You should use ; to join each path.
  2. Open the client and navigate to the settings page. Enter the path including the dependencies binaries you got from step 1 into the “Extra Path” textbox and click “Save”.
  3. Verify that the client can read the dependencies by navigating to the “Environment Information” page.

MiniConda

Microsoft Visual C+ + Redistributable