update install guide

README.md

@@ -12,6 +12,7 @@ See the [installation guide](docs/installguide.md) for more details, but:
 git clone --recursive https://github.com/PolusAI/workflow-inference-compiler.git
 cd workflow-inference-compiler
 ./install_conda.sh  # install_conda.bat on Windows
+source ~/.bashrc
 conda create --name wic
 conda activate wic
 ./install_system_deps.sh  # install_system_deps.bat on Windows

docs/installguide.md

@@ -48,6 +48,20 @@ When running Docker for Mac, in some cases execution will hang. See [all contain
 
 If you are experiencing hanging, and if the command `ps aux | grep com.docker | wc -l` returns more than 1000, this is likely the issue. If restarting Docker via the GUI doesn't work, try `sudo pkill com.docker && sudo pkill Docker`.
 
+## podman
+
+Alternatively, instead of docker you can use [podman](https://podman.io/whatis.html). podman is a daemonless (more secure) way to run containers. On linux, you can install podman via conda `conda install -c conda-forge podman` or using distro-specific methods. To run workflows with podman, simply append `--user_space_docker_cmd podman` after `--run_local`.
+
+## Installation on Windows
+
+Although compiling workflows natively on Windows is supported, the underlying `cwltool` runner currently requires [Windows Subsystem for Linux](https://learn.microsoft.com/en-us/windows/wsl/install#install-wsl-command). To install WSL, simply open PowerShell or Windows Command Prompt in **administrator** mode and run the command `wsl --install`. For more information about WSL, see the official [FAQ](https://learn.microsoft.com/en-us/windows/wsl/faq).
+
+To install podman inside of WSL, simply run (from inside WSL) `sudo apt-get update && sudo apt-get install uidmap podman`.
+
+### known issues
+
+Network performance on WSL can be [very slow](https://github.com/microsoft/WSL/issues/4901). This appears to be caused by the "Large Send Offload Version 2" network setting. See [this article](https://townsyio.medium.com/wsl2-how-to-fix-download-speed-3edb0c348e29) for how to disable this setting.
+
 ## conda
 
 [conda](https://en.wikipedia.org/wiki/Conda_(package_manager)) is an open source, cross platform package management system. It can install both Python dependencies and system binary dependencies, so conda is essentially a replacement for `pip`. The associated package distributions named `anaconda` and `miniconda` provide a database of packages that can be used with the `conda` command. (There is also an open source package distribution called [conda-forge](https://conda-forge.org)) Either one works, so if you already have anaconda installed then great. Otherwise, [miniconda](https://docs.conda.io/en/latest/miniconda.html) is all you need.
@@ -56,6 +70,7 @@ You can install conda and the system dependencies with the following commands:
 
 ```
 ./install_conda.sh  # install_conda.bat on Windows
+source ~/.bashrc
 conda create --name wic
 conda activate wic
 ./install_system_deps.sh  # install_system_deps.bat on Windows
@@ -94,6 +109,10 @@ conda activate vis
 pip install -e ".[all]"
 ```
 
+## CUDA
+
+Some of the workflows require an Nvidia CUDA GPU. Please see the Nvidia [installation guides](https://docs.nvidia.com/cuda/#installation-guides) for more information.
+
 ## testing
 
 To test your installation, you can run the example in README.md:

install_conda.bat

@@ -1,4 +1,4 @@
 set CONDA="Mambaforge-pypy3-Windows-x86_64.exe"
 curl -L -O https://github.com/conda-forge/miniforge/releases/latest/download/%CONDA%
 %CONDA%
-rm -f %CONDA%
+del %CONDA%

install_conda.sh

@@ -3,4 +3,5 @@ CONDA="Mambaforge-pypy3-$(uname)-$(uname -m).sh"
 curl -L -O  https://github.com/conda-forge/miniforge/releases/latest/download/"$CONDA"
 chmod +x "$CONDA"
 ./"$CONDA" -b
+~/mambaforge-pypy3/bin/mamba init
 rm -f "$CONDA"