From f7179a51a191cd0d3efe2fdb462e6160dae02546 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Maren=20B=C3=BCttner?= Date: Fri, 23 Sep 2022 10:57:21 +0200 Subject: [PATCH 1/5] Update sc_tutorial_environment.yml --- sc_tutorial_environment.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/sc_tutorial_environment.yml b/sc_tutorial_environment.yml index 97a8ac0..c35cfe6 100644 --- a/sc_tutorial_environment.yml +++ b/sc_tutorial_environment.yml @@ -3,7 +3,7 @@ channels: - conda-forge - bioconda dependencies: - - python>=3.5, <3.7 + - python>=3.8 - cmake>=3.9, <3.11 - r-essentials - r-rgl @@ -38,6 +38,6 @@ dependencies: - fa2 - gprofiler-official - scanpy - - rpy2 + - rpy2==3.4.2 - git+https://github.com/flying-sheep/anndata2ri From 89206df532254d0ad58210fd3c9673a2158b49a2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Maren=20B=C3=BCttner?= Date: Fri, 23 Sep 2022 10:59:59 +0200 Subject: [PATCH 2/5] update Readme.md Update bioconductor version, add scrublet and DropletUtils packages --- README.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 400e45a..cb91b79 100644 --- a/README.md +++ b/README.md @@ -89,7 +89,7 @@ To set up a conda environment, the following instructions must be followed. ``` install.packages(c('devtools', 'gam', 'RColorBrewer', 'BiocManager')) update.packages(ask=F) - BiocManager::install(c("scran","MAST","monocle","ComplexHeatmap","slingshot"), version = "3.8") + BiocManager::install(c("scran","MAST","monocle","ComplexHeatmap","slingshot", "DropletUtils"), version = "3.15") ``` These steps should set up an environment to perform single cell analysis with the tutorial workflow on a Linux system. Please note that we have encountered issues with conda environments on Mac OS. When using Mac OS we recommend installing the packages without conda using separately installed `python` and `R` versions. Alternatively, you can try using the base conda environment and installing all packages as described in the `conda_env_instructions_for_mac.txt` file. In the base environment, R should be able to find the relevant gsl libraries, so `LDFLAGS` and `CFLAGS` should not need to be set. @@ -148,7 +148,7 @@ General: - Jupyter notebook - IRKernel - rpy2 -- R >= 3.4.3 +- R >= 4.0 - Python >= 3.5 Python: @@ -199,4 +199,4 @@ Ensure that the correct g:profiler package is used for the notebook. Notebooks u #### If not R packages can be found: -Ensure that IRkernel has linked the correct version of R with your jupyter notebook. Check instructions at `https://github.com/IRkernel/IRkernel`. \ No newline at end of file +Ensure that IRkernel has linked the correct version of R with your jupyter notebook. Check instructions at `https://github.com/IRkernel/IRkernel`. From 86307728af11d005cf8b0da96f03677f1e50f959 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Maren=20B=C3=BCttner?= Date: Fri, 23 Sep 2022 11:11:26 +0200 Subject: [PATCH 3/5] update conda and mac instructions --- conda_env_instructions_for_mac.md | 24 ++++++++++++++++++++---- 1 file changed, 20 insertions(+), 4 deletions(-) diff --git a/conda_env_instructions_for_mac.md b/conda_env_instructions_for_mac.md index aaad9c0..80a46f9 100644 --- a/conda_env_instructions_for_mac.md +++ b/conda_env_instructions_for_mac.md @@ -1,19 +1,35 @@ -# 1. Install miniconda or anaconda with python version 3.6 or above. +# 1. Install miniconda or anaconda with python version 3.8 or above. # 2. Run the following commands for conda and pip conda update --all conda install r-essentials r-rgl conda install pandas numpy scipy scikit-learn jupyter gsl tzlocal simplegeneric natsort h5py tqdm patsy llvmlite numba networkx joblib numexpr pytables seaborn statsmodels pip - conda install -c conda-forge python-igraph louvain + conda install -c conda-forge python-igraph louvain leiden pip install --upgrade pip - pip install MulticoreTSNE anndata anndata2ri fa2 gprofiler-official scanpy rpy2 + pip install MulticoreTSNE anndata anndata2ri fa2 gprofiler-official scanpy rpy2 scrublet `MulticoreTSNE` is optional and just for speed, so leave it out if you run into problems installing it. + # 3. Start R and run the following commands: install.packages(c('devtools', 'gam', 'RColorBrewer', 'BiocManager')) update.packages(ask=F) - BiocManager::install(c("scran","MAST","monocle","ComplexHeatmap","slingshot"), version = "3.8") + BiocManager::install(c("scran","MAST","monocle","ComplexHeatmap","slingshot", "DropletUtils"), version = "3.15") + +The version of the `BiocManager` may depend on the installed R version (here `R>=4.2`). + +# Troubleshooting + +## MulticoreTSNE +A current workaround (as of 23/09/2022) to install `MulticoreTSNE` is to clone the `git` repository, adjust the `setup.py` and install manually as follows (solution provided by [Lisa Barros](https://github.com/lisa-sousa): + +``` +git clone https://github.com/DmitryUlyanov/Multicore-TSNE.git +``` +Then open the `setup.py` and replace `self.cmake_args or "--",` by `self.cmake_args or "",`. Install via +``` +python setup.py install +``` From bf9fcb956a7cf4af1593fecad400cd31181446c2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Maren=20B=C3=BCttner?= Date: Fri, 23 Sep 2022 11:12:10 +0200 Subject: [PATCH 4/5] fix typo --- conda_env_instructions_for_mac.md | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/conda_env_instructions_for_mac.md b/conda_env_instructions_for_mac.md index 80a46f9..e5309cd 100644 --- a/conda_env_instructions_for_mac.md +++ b/conda_env_instructions_for_mac.md @@ -24,12 +24,14 @@ The version of the `BiocManager` may depend on the installed R version (here `R> # Troubleshooting ## MulticoreTSNE -A current workaround (as of 23/09/2022) to install `MulticoreTSNE` is to clone the `git` repository, adjust the `setup.py` and install manually as follows (solution provided by [Lisa Barros](https://github.com/lisa-sousa): +A current workaround (as of 23/09/2022) to install `MulticoreTSNE` is to clone the `git` repository, adjust the `setup.py` and install manually as follows (solution provided by [Lisa Barros](https://github.com/lisa-sousa)): ``` git clone https://github.com/DmitryUlyanov/Multicore-TSNE.git ``` -Then open the `setup.py` and replace `self.cmake_args or "--",` by `self.cmake_args or "",`. Install via +Then open the `setup.py` and replace `self.cmake_args or "--",` by `self.cmake_args or "",`. + +Then install via ``` python setup.py install ``` From 3544602e31bf36535f803939cdf87af4b820b57d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Maren=20B=C3=BCttner?= Date: Thu, 20 Oct 2022 10:36:38 +0200 Subject: [PATCH 5/5] update leiden installation --- conda_env_instructions_for_mac.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conda_env_instructions_for_mac.md b/conda_env_instructions_for_mac.md index e5309cd..df5c878 100644 --- a/conda_env_instructions_for_mac.md +++ b/conda_env_instructions_for_mac.md @@ -5,7 +5,7 @@ conda update --all conda install r-essentials r-rgl conda install pandas numpy scipy scikit-learn jupyter gsl tzlocal simplegeneric natsort h5py tqdm patsy llvmlite numba networkx joblib numexpr pytables seaborn statsmodels pip - conda install -c conda-forge python-igraph louvain leiden + conda install -c conda-forge python-igraph louvain leidenalg pip install --upgrade pip pip install MulticoreTSNE anndata anndata2ri fa2 gprofiler-official scanpy rpy2 scrublet