From b8ea72a661881394c4847ce93308788ca2f59e9d Mon Sep 17 00:00:00 2001 From: Lilly Date: Tue, 2 Apr 2024 15:32:06 +0200 Subject: [PATCH 1/8] Updated installation instructions --- README.md | 18 +++++++++--------- docs/install.md | 41 ++++++++++++++++++++++++++++++++--------- 2 files changed, 41 insertions(+), 18 deletions(-) diff --git a/README.md b/README.md index 8edf9773..dc1af922 100644 --- a/README.md +++ b/README.md @@ -25,24 +25,24 @@ Available workflows: ## Installation and configuration -See [installation instructions here](https://panpipes-pipelines.readthedocs.io/en/latest/install.html) +For detailed installation instructions (including those for Apple Silicon machines), refer to the [installation instructions here](https://panpipes-pipelines.readthedocs.io/en/latest/install.html). -We recommend installing panpipes in a conda environment, we provide a minimal conda config file in `pipeline_env.yaml` +We recommend installing panpipes in a conda environment. +For that, we provide a minimal conda config file in `pipeline_env.yaml`. +First, clone this repository and navigate to the root directory of the repository: ``` -conda env create --file=pipeline_env.yaml +git clone https://github.com/DendrouLab/panpipes.git +cd panpipes ``` -In this environment, you can install nightly version of panpipes, i.e. cloning this repo and installing it from main. +Then, create the conda environment and install the nightly version of panpipes using the following command: ``` -git clone https://github.com/DendrouLab/panpipes.git -cd panpipes -pip install -e . +conda env create --file=pipeline_env.yaml ``` - -Oxford BMRC Rescomp users find additional advice in [docs/installation_rescomp](https://github.com/DendrouLab/panpipes/blob/main/docs/installation_rescomp.md) +Oxford BMRC Rescomp users find additional advice on the installation [here](https://github.com/DendrouLab/panpipes/blob/main/docs/installation_rescomp.md). ## Releases diff --git a/docs/install.md b/docs/install.md index b98f9953..35d5c74c 100644 --- a/docs/install.md +++ b/docs/install.md @@ -1,15 +1,38 @@ # Installation of panpipes -## Create virtual environment +>Note: Oxford BMRC Rescomp users find additional advice on the installation [here](https://github.com/DendrouLab/panpipes/blob/main/docs/installation_rescomp.md). + +## Create virtual environment and install panpipes We recommend running panpipes within a virtual environment to prevent conflicts. -### Option 1: create conda environment (Recommended) +### Option 1: Installation in conda environment (Recommended) >Note: For installation instructions on Apple machines with M chips, scroll down. -To Run panpipes, we install it in a conda environment with R and python. +To run panpipes, we install it in a conda environment with R and python. Panpipes has a lot of dependencies, so you may want to consider the faster [`mamba`](https://mamba.readthedocs.io/en/latest/index.html) instead of `conda` for installation. +Panpipes can be installed via different methods, either from PyPi or from the Github repository. +We recommend using Option 1.1 to install the nightly version of panpipes. + +#### Option 1.1: Nightly panpipes version with preconfigured conda config file (Recommended) +We recommend installing a nightly version of panpipes. +For that, we provide a minimal conda config file in `pipeline_env.yaml`. +First, clone this repository and navigate to the root directory of the repository: + +``` +git clone https://github.com/DendrouLab/panpipes.git +cd panpipes +``` + +Then, create the conda environment and install the nightly version of panpipes using the following command: + +``` +conda env create --file=pipeline_env.yaml +``` + +#### Option 1.2: Manual conda environment creation +As an alternative to the preconfigured conda environment, you can create a conda environment manually. ```bash #This follows the suggestions made here: [https://www.biostars.org/p/498049/](https://www.biostars.org/p/498049/) @@ -20,21 +43,21 @@ conda search r-base conda create --name pipeline_env python=3.10 r-base=4.3.0 ``` -now we activate the environment +Next, we activate the environment: ```bash conda activate pipeline_env ``` -Let's first install the R packages +Let's first install the R packages: ```bash conda install -c conda-forge r-tidyverse r-optparse r-ggforce r-ggraph r-xtable r-hdf5r r-clustree r-cowplot ``` -Then we can install panpipes: +Finally, we install panpipes, which you can install either from PyPi or from the Github repository. -#### 1. Installing panpipes from PyPi +##### Installing panpipes from PyPi You can install `panpipes` directly from `PyPi` with: @@ -49,9 +72,9 @@ pip install 'panpipes[spatial]' ``` The extra `[spatial]` includes squidpy, cell2location, and tangram-sc packages. -#### 2. Nightly versions of panpipes +##### Nightly versions of panpipes -If you prefer to use the most recent dev version, install from Github +If you prefer to use the most recent dev version, install panpipes from Github: ```bash git clone https://github.com/DendrouLab/panpipes From 17a0eb2f20c4e987bfb556e983e1012c90fe3572 Mon Sep 17 00:00:00 2001 From: Lilly Date: Tue, 2 Apr 2024 15:38:31 +0200 Subject: [PATCH 2/8] Added dependency installation recommendations --- README.md | 4 +++- docs/install.md | 4 +++- 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index dc1af922..45c7e4c1 100644 --- a/README.md +++ b/README.md @@ -40,13 +40,15 @@ Then, create the conda environment and install the nightly version of panpipes u ``` conda env create --file=pipeline_env.yaml +conda activate pipeline_env +pip install -e . ``` Oxford BMRC Rescomp users find additional advice on the installation [here](https://github.com/DendrouLab/panpipes/blob/main/docs/installation_rescomp.md). ## Releases -Since `panpipes v0.4.0` ,the `ingest` workflow expects different headers for the RNA and Protein modalities from the previous releases. +Since `panpipes v0.4.0`, the `ingest` workflow expects different headers for the RNA and Protein modalities from the previous releases. Check the example [submission file](https://github.com/DendrouLab/panpipes/blob/main/docs/usage/sample_file_qc_mm.md) and the [documentation](https://panpipes-pipelines.readthedocs.io/en/latest/usage/setup_for_qc_mm.html) for more detailed instructions. ## Citation diff --git a/docs/install.md b/docs/install.md index 35d5c74c..b3ea828d 100644 --- a/docs/install.md +++ b/docs/install.md @@ -29,6 +29,8 @@ Then, create the conda environment and install the nightly version of panpipes u ``` conda env create --file=pipeline_env.yaml +conda activate pipeline_env +pip install -e . ``` #### Option 1.2: Manual conda environment creation @@ -72,7 +74,7 @@ pip install 'panpipes[spatial]' ``` The extra `[spatial]` includes squidpy, cell2location, and tangram-sc packages. -##### Nightly versions of panpipes +##### Nightly version of panpipes If you prefer to use the most recent dev version, install panpipes from Github: From bbf34649bad11bc08f29dc1d2f1ffa25155412df Mon Sep 17 00:00:00 2001 From: Lilly Date: Wed, 3 Apr 2024 10:56:54 +0200 Subject: [PATCH 3/8] Simplified installation instructions --- README.md | 4 +- docs/install.md | 168 +++++++++++++++++++++++------------------------- 2 files changed, 83 insertions(+), 89 deletions(-) diff --git a/README.md b/README.md index 45c7e4c1..d4e9338b 100644 --- a/README.md +++ b/README.md @@ -31,14 +31,14 @@ We recommend installing panpipes in a conda environment. For that, we provide a minimal conda config file in `pipeline_env.yaml`. First, clone this repository and navigate to the root directory of the repository: -``` +```bash git clone https://github.com/DendrouLab/panpipes.git cd panpipes ``` Then, create the conda environment and install the nightly version of panpipes using the following command: -``` +```bash conda env create --file=pipeline_env.yaml conda activate pipeline_env pip install -e . diff --git a/docs/install.md b/docs/install.md index b3ea828d..890523ac 100644 --- a/docs/install.md +++ b/docs/install.md @@ -3,38 +3,19 @@ >Note: Oxford BMRC Rescomp users find additional advice on the installation [here](https://github.com/DendrouLab/panpipes/blob/main/docs/installation_rescomp.md). -## Create virtual environment and install panpipes - We recommend running panpipes within a virtual environment to prevent conflicts. +In the following, we provide instructions on how to do this using conda, mamba, or python venv. -### Option 1: Installation in conda environment (Recommended) >Note: For installation instructions on Apple machines with M chips, scroll down. +## Option 1: Installation in manually configured conda environment To run panpipes, we install it in a conda environment with R and python. Panpipes has a lot of dependencies, so you may want to consider the faster [`mamba`](https://mamba.readthedocs.io/en/latest/index.html) instead of `conda` for installation. -Panpipes can be installed via different methods, either from PyPi or from the Github repository. -We recommend using Option 1.1 to install the nightly version of panpipes. - -#### Option 1.1: Nightly panpipes version with preconfigured conda config file (Recommended) -We recommend installing a nightly version of panpipes. -For that, we provide a minimal conda config file in `pipeline_env.yaml`. -First, clone this repository and navigate to the root directory of the repository: - -``` -git clone https://github.com/DendrouLab/panpipes.git -cd panpipes -``` - -Then, create the conda environment and install the nightly version of panpipes using the following command: - -``` -conda env create --file=pipeline_env.yaml -conda activate pipeline_env -pip install -e . -``` +Panpipes can be installed via different methods, either from `PyPi` or from the Github repository. +Option 1 describes the installation via `PyPi` in a manually configured conda environment (no cloning of the repository necessary). -#### Option 1.2: Manual conda environment creation -As an alternative to the preconfigured conda environment, you can create a conda environment manually. +### Create conda environment +First, create a conda environment to run panpipes in: ```bash #This follows the suggestions made here: [https://www.biostars.org/p/498049/](https://www.biostars.org/p/498049/) @@ -57,13 +38,12 @@ Let's first install the R packages: conda install -c conda-forge r-tidyverse r-optparse r-ggforce r-ggraph r-xtable r-hdf5r r-clustree r-cowplot ``` -Finally, we install panpipes, which you can install either from PyPi or from the Github repository. - -##### Installing panpipes from PyPi - -You can install `panpipes` directly from `PyPi` with: +### Install panpipes +Finally, we install panpipes. +You can install it either from `PyPi` (shown here) or a nightly version from the Github repository (shown in Option 2): ```bash +# Install panpipes from PyPi pip install panpipes ``` @@ -72,15 +52,27 @@ If you intend to use panpipes for spatial analysis, instead install: ```bash pip install 'panpipes[spatial]' ``` -The extra `[spatial]` includes squidpy, cell2location, and tangram-sc packages. +The extra `[spatial]` includes the `squidpy`, `cell2location`, and `tangram-sc` packages. + -##### Nightly version of panpipes +## Option 2: Install nightly panpipes version with preconfigured conda config file -If you prefer to use the most recent dev version, install panpipes from Github: +If you prefer to use the most recent development version, install panpipes the nightly version from the Github repository. +To make the installation easier, we provide a minimal conda config file in `pipeline_env.yaml`. +First, clone the [panpipes repository](https://github.com/DendrouLab/panpipes) and navigate to the root directory of the repository: +### Clone the repository ```bash -git clone https://github.com/DendrouLab/panpipes +git clone https://github.com/DendrouLab/panpipes.git cd panpipes +``` + +### Create conda environment and install nightly panpipes version +Then, create the conda environment and install the nightly version of panpipes using the following command: + +```bash +conda env create --file=pipeline_env.yaml +conda activate pipeline_env pip install -e . ``` @@ -97,73 +89,31 @@ or apt-get install time ``` -#### Installation on Apple Silicon M chips -If you intend to install panpipes via conda on a macOS machine with M-Chip, you might face issues when installing or using certain workflows of panpipes. -This is because panpipes relies on [scvi-tools], which currently only supports execution on Apple Silicon machines when installed using a native Python version (owing to a dependency on JAX). - -Follow these steps to install pertpy on an Apple Silicon machine: - -1. Install [Homebrew](https://brew.sh/) - -2. Install Apple Silicon version of Mambaforge (If you already have Anaconda/Miniconda installed, make sure - having both mamba and conda won't cause conflicts). Additionally, we need clang which is included in llvm, so we install that as well. - -```bash -brew install --cask mambaforge -brew install llvm -``` - -3. Create a new environment using mamba (here with python 3.10) and activate it - -```bash -conda config --add channels conda-forge -conda config --set channel_priority strict -# you should remove the strict priority afterwards! -mamba search r-base -mamba create --name pipeline_env -mamba activate pipeline_env -``` - -4. Add the osx-64 channel to the environment, then install Python and R -Because not all R packages are available via the ARM64 channel, we need to specify the osx-64 channel to install all required R packages. - -```bash -conda config --env --set subdir osx-64 -mamba install python=3.10 r-base=4.3.0 -``` - -5. Install dependencies - -```bash -conda install -c conda-forge r-tidyverse r-optparse r-ggforce r-ggraph r-xtable r-hdf5r r-clustree r-cowplot -pip install panpipes -``` - - -### Option 2: python venv environment +## Option 3: python venv environment +As an alternative to conda, you can use a python virtual environment. Navigate to where you want to create your virtual environment and follow the steps below to create a pip virtual environment. ```bash +# Create a panpipes/venv folder python3 -m venv --prompt=panpipes python3-venv-panpipes/ -# This will create a panpipes/venv folder ``` -Activate the environment +Activate the environment: ```bash source python3-venv-panpipes/bin/activate ``` -As explained in the conda installation, you can install `panpipes` with: +As explained above, you can install panpipes from `PyPi` with: ```bash pip install panpipes ``` -or install a nightly version of panpipes by cloning the Github repository. +Alternatively, you can install a nightly version of panpipes by cloning the Github repository (see above for instructions). -#### R packages installation in python venv +### R packages installation in python venv If you are using a venv virtual environment, the pipeline will call a local R installation, so make sure R is installed and install the required packages with the command we provide below. (This executable requires that you specify a CRAN mirror in your `.Rprofile`). @@ -185,9 +135,9 @@ If you want more control over your installation use the [script on github](https Running with the option `--vanilla` or `--no-site-file` prevents R from reading your `.Renvironment` or `.Rprofile` in case you want to use different settings from you local R installation. You can expect the installation of R libraries to take quite some time, this is not something related to `panpipes` but how R manages their libraries and dependencies! -#### Check installation +### Check installation -To check the installation was successful run the following line +To check the installation was successful, run the following line: ```bash panpipes --help @@ -198,10 +148,54 @@ A list of available pipelines should appear! You're all set to run `panpipes` on your local machine. If you want to configure it on a HPC server, follow the next instructions. +## Installation on Apple Silicon M chips +If you intend to install panpipes via conda on a macOS machine with M-Chip, you might face issues when installing or using certain workflows of panpipes. +This is because panpipes relies on [scvi-tools], which currently only supports execution on Apple Silicon machines when installed using a native Python version (owing to a dependency on JAX). + +Follow these steps to install pertpy on an Apple Silicon machine: + +1. Install [Homebrew](https://brew.sh/) + +2. Install Apple Silicon version of Mambaforge (If you already have Anaconda/Miniconda installed, make sure + having both mamba and conda won't cause conflicts). Additionally, we need clang which is included in llvm, so we install that as well. + +```bash +brew install --cask mambaforge +brew install llvm +``` + +3. Create a new environment using mamba (here with python 3.10) and activate it + +```bash +conda config --add channels conda-forge +conda config --set channel_priority strict +# you should remove the strict priority afterwards! +mamba search r-base +mamba create --name pipeline_env +mamba activate pipeline_env +``` + +4. Add the osx-64 channel to the environment, then install Python and R +Because not all R packages are available via the ARM64 channel, we need to specify the osx-64 channel to install all required R packages. + +```bash +conda config --env --set subdir osx-64 +mamba install python=3.10 r-base=4.3.0 +``` + +5. Install dependencies + +```bash +conda install -c conda-forge r-tidyverse r-optparse r-ggforce r-ggraph r-xtable r-hdf5r r-clustree r-cowplot +pip install panpipes +``` + + ## Pipeline configuration for HPC clusters -(For SGE or SLURM clusters) -*Note: You only need this configuration step if you want to use an HPC to dispatch individual task as separate parallel jobs. You won't need this for a local installation of panpipes.* +This section is for users who want to run panpipes on a High-Performance Computing (HPC) cluster with a job scheduler like SGE or SLURM. + +>Note: You only need this configuration step if you want to use an HPC to dispatch individual task as separate parallel jobs. You won't need this for a local installation of panpipes. Create a yml file for the cgat core pipeline software to read From 1ed54ddd5400936799469929f38b5c6ecfd5d270 Mon Sep 17 00:00:00 2001 From: Lilly Date: Wed, 3 Apr 2024 11:10:31 +0200 Subject: [PATCH 4/8] Improved text and fixed typos --- docs/install.md | 34 ++++++++++++++++++---------------- 1 file changed, 18 insertions(+), 16 deletions(-) diff --git a/docs/install.md b/docs/install.md index 890523ac..0f2660b1 100644 --- a/docs/install.md +++ b/docs/install.md @@ -1,12 +1,12 @@ # Installation of panpipes ->Note: Oxford BMRC Rescomp users find additional advice on the installation [here](https://github.com/DendrouLab/panpipes/blob/main/docs/installation_rescomp.md). - We recommend running panpipes within a virtual environment to prevent conflicts. In the following, we provide instructions on how to do this using conda, mamba, or python venv. ->Note: For installation instructions on Apple machines with M chips, scroll down. +> **Note**: For installation instructions on Apple machines with M chips, scroll down. + +> **Note**: Oxford BMRC Rescomp users find additional advice on the installation [here](https://github.com/DendrouLab/panpipes/blob/main/docs/installation_rescomp.md). ## Option 1: Installation in manually configured conda environment To run panpipes, we install it in a conda environment with R and python. @@ -57,11 +57,12 @@ The extra `[spatial]` includes the `squidpy`, `cell2location`, and `tangram-sc` ## Option 2: Install nightly panpipes version with preconfigured conda config file -If you prefer to use the most recent development version, install panpipes the nightly version from the Github repository. +If you prefer to use the most recent development version, install the nightly panpipes version from the Github repository. To make the installation easier, we provide a minimal conda config file in `pipeline_env.yaml`. -First, clone the [panpipes repository](https://github.com/DendrouLab/panpipes) and navigate to the root directory of the repository: ### Clone the repository +First, clone the [panpipes repository](https://github.com/DendrouLab/panpipes) and navigate to the root directory of the repository: + ```bash git clone https://github.com/DendrouLab/panpipes.git cd panpipes @@ -77,7 +78,8 @@ pip install -e . ``` Panpipes requires the unix package `time`. -You can check if it installed with `dpkg-query -W time`. If time not already installed, you can +You can check if it installed with `dpkg-query -W time`. +If `time` is not already installed, you can install it using: ```bash conda install time @@ -91,8 +93,8 @@ apt-get install time ## Option 3: python venv environment -As an alternative to conda, you can use a python virtual environment. -Navigate to where you want to create your virtual environment and follow the steps below to create a pip virtual environment. +As an alternative to a conda environment, you can also install panpipes in a python virtual environment. +Navigate to where you want to create your virtual environment and follow the steps below to create a `pip` virtual environment. ```bash # Create a panpipes/venv folder @@ -111,7 +113,7 @@ As explained above, you can install panpipes from `PyPi` with: pip install panpipes ``` -Alternatively, you can install a nightly version of panpipes by cloning the Github repository (see above for instructions). +Alternatively, you can install a nightly version of panpipes by cloning the Github repository (see instructions above). ### R packages installation in python venv @@ -119,7 +121,7 @@ If you are using a venv virtual environment, the pipeline will call a local R in (This executable requires that you specify a CRAN mirror in your `.Rprofile`). for example, add this line to your `.Rprofile` to automatically fetch the preferred mirror: -*remember to customise with your preferred [R mirror](https://cran.r-project.org/mirrors.html).* +> **Note:** Remember to customise with your preferred [R mirror](https://cran.r-project.org/mirrors.html). ```R options(repos = c(CRAN="https://cran.uni-muenster.de/")) @@ -150,21 +152,21 @@ If you want to configure it on a HPC server, follow the next instructions. ## Installation on Apple Silicon M chips If you intend to install panpipes via conda on a macOS machine with M-Chip, you might face issues when installing or using certain workflows of panpipes. -This is because panpipes relies on [scvi-tools], which currently only supports execution on Apple Silicon machines when installed using a native Python version (owing to a dependency on JAX). +This is because panpipes relies on `scvi-tools`, which currently [only supports execution on Apple Silicon machines when installed using a native Python version](https://docs.scvi-tools.org/en/stable/installation.html#apple-silicon) (due to a dependency on JAX). -Follow these steps to install pertpy on an Apple Silicon machine: +Follow these steps to install panpipes on an Apple Silicon machine: 1. Install [Homebrew](https://brew.sh/) 2. Install Apple Silicon version of Mambaforge (If you already have Anaconda/Miniconda installed, make sure - having both mamba and conda won't cause conflicts). Additionally, we need clang which is included in llvm, so we install that as well. + having both mamba and conda won't cause conflicts). Additionally, we need clang which is included in llvm, so we install that as well: ```bash brew install --cask mambaforge brew install llvm ``` -3. Create a new environment using mamba (here with python 3.10) and activate it +3. Create a new environment using mamba (here with python 3.10) and activate it: ```bash conda config --add channels conda-forge @@ -176,14 +178,14 @@ mamba activate pipeline_env ``` 4. Add the osx-64 channel to the environment, then install Python and R -Because not all R packages are available via the ARM64 channel, we need to specify the osx-64 channel to install all required R packages. +Because not all R packages are available via the ARM64 channel, we need to specify the osx-64 channel to install all required R packages: ```bash conda config --env --set subdir osx-64 mamba install python=3.10 r-base=4.3.0 ``` -5. Install dependencies +5. Install R dependencies and panpipes itself: ```bash conda install -c conda-forge r-tidyverse r-optparse r-ggforce r-ggraph r-xtable r-hdf5r r-clustree r-cowplot From 5ca39d14d8e316dcea2f4748b257138791c981a4 Mon Sep 17 00:00:00 2001 From: bio-la Date: Mon, 22 Apr 2024 16:33:56 +0200 Subject: [PATCH 5/8] minor fixes --- docs/install.md | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/docs/install.md b/docs/install.md index 0f2660b1..16576dda 100644 --- a/docs/install.md +++ b/docs/install.md @@ -76,6 +76,11 @@ conda env create --file=pipeline_env.yaml conda activate pipeline_env pip install -e . ``` +To install the spatial dependencies from the repo, use + +```bash +pip install .[spatial] +``` Panpipes requires the unix package `time`. You can check if it installed with `dpkg-query -W time`. @@ -147,8 +152,6 @@ panpipes --help A list of available pipelines should appear! -You're all set to run `panpipes` on your local machine. -If you want to configure it on a HPC server, follow the next instructions. ## Installation on Apple Silicon M chips If you intend to install panpipes via conda on a macOS machine with M-Chip, you might face issues when installing or using certain workflows of panpipes. @@ -191,7 +194,8 @@ mamba install python=3.10 r-base=4.3.0 conda install -c conda-forge r-tidyverse r-optparse r-ggforce r-ggraph r-xtable r-hdf5r r-clustree r-cowplot pip install panpipes ``` - +You're all set to run `panpipes` on your local machine. +If you want to configure it on a HPC server, follow the next instructions. ## Pipeline configuration for HPC clusters From da89f2cf5a1a5c60be401ad343add3be24b3f519 Mon Sep 17 00:00:00 2001 From: bio-la Date: Mon, 22 Apr 2024 16:36:37 +0200 Subject: [PATCH 6/8] small --- docs/install.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/docs/install.md b/docs/install.md index 16576dda..03b1270f 100644 --- a/docs/install.md +++ b/docs/install.md @@ -194,6 +194,8 @@ mamba install python=3.10 r-base=4.3.0 conda install -c conda-forge r-tidyverse r-optparse r-ggforce r-ggraph r-xtable r-hdf5r r-clustree r-cowplot pip install panpipes ``` + + You're all set to run `panpipes` on your local machine. If you want to configure it on a HPC server, follow the next instructions. From fd7dd7e47dfe49acfe8e7899ea0e9c112de419c8 Mon Sep 17 00:00:00 2001 From: Lilly Date: Mon, 22 Apr 2024 17:36:51 +0200 Subject: [PATCH 7/8] Add note for Windows machines --- docs/install.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/install.md b/docs/install.md index 03b1270f..cbe7b816 100644 --- a/docs/install.md +++ b/docs/install.md @@ -4,9 +4,9 @@ We recommend running panpipes within a virtual environment to prevent conflicts. In the following, we provide instructions on how to do this using conda, mamba, or python venv. -> **Note**: For installation instructions on Apple machines with M chips, scroll down. - -> **Note**: Oxford BMRC Rescomp users find additional advice on the installation [here](https://github.com/DendrouLab/panpipes/blob/main/docs/installation_rescomp.md). +> **Note**: For installation instructions on **Apple machines with M chips**, scroll down. +> If you are working on a **Windows** machine, please use Windows Subsystem for Linux (WSL) to run panpipes in order to have access to the latest r-base version. +> **Oxford BMRC Rescomp** users find additional advice on the installation [here](https://github.com/DendrouLab/panpipes/blob/main/docs/installation_rescomp.md). ## Option 1: Installation in manually configured conda environment To run panpipes, we install it in a conda environment with R and python. From a106e8b957d365cb6d93bec04ea6474ea2d84ace Mon Sep 17 00:00:00 2001 From: Lilly Date: Mon, 22 Apr 2024 17:44:22 +0200 Subject: [PATCH 8/8] Fixed link --- docs/install.md | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/docs/install.md b/docs/install.md index cbe7b816..cf4d0746 100644 --- a/docs/install.md +++ b/docs/install.md @@ -15,10 +15,9 @@ Panpipes can be installed via different methods, either from `PyPi` or from the Option 1 describes the installation via `PyPi` in a manually configured conda environment (no cloning of the repository necessary). ### Create conda environment -First, create a conda environment to run panpipes in: +First, create a conda environment to run panpipes in. For that, we replicate the suggestions made [here](https://www.biostars.org/p/498049/): -```bash -#This follows the suggestions made here: [https://www.biostars.org/p/498049/](https://www.biostars.org/p/498049/) +```bash conda config --add channels conda-forge conda config --set channel_priority strict # you should remove the strict priority afterwards!