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: