From a3e86594db263d7781c0d99ec50172576a61dc2c Mon Sep 17 00:00:00 2001 From: bio-la Date: Sun, 17 Sep 2023 15:37:40 +0200 Subject: [PATCH 1/2] modify installation --- docs/install.md | 44 ++++++++++++++++++++++++++------------------ 1 file changed, 26 insertions(+), 18 deletions(-) diff --git a/docs/install.md b/docs/install.md index 6eb4cd5c..b47d4278 100644 --- a/docs/install.md +++ b/docs/install.md @@ -1,24 +1,7 @@ # Installation of panpipes -## Step 1 -Panpipes requires the unix package `time`, -you can check if it install ed with -``` -dpkg-query -W time -``` - -if this is not already installed on your system install it with: -``` -apt-get install time -``` - -Alternatively: -``` -conda install time -``` - -## Step 2: create virtual environment +## Step 1: create virtual environment We recommend running panpipes within a virtual environment to maintain reproducibility @@ -54,6 +37,31 @@ Install R packages conda install -c conda-forge r-tidyverse r-optparse r-ggforce r-ggraph r-xtable r-hdf5r r-clustree ``` +Panpipes requires the unix package `time`, in conda you can install it with: + +You can check if it installed with + +``` +dpkg-query -W time +``` +if this is not already installed on your conda env with: + +``` +conda install time +``` +or + +``` +apt-get install time +``` + + + + + + + + Download and install panpipes ``` pip install panpipes From 60e6fbe4ec554111083c36b325dc176775688a89 Mon Sep 17 00:00:00 2001 From: bio-la Date: Sun, 17 Sep 2023 15:43:42 +0200 Subject: [PATCH 2/2] order of sentences --- docs/install.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/docs/install.md b/docs/install.md index b47d4278..3bc21363 100644 --- a/docs/install.md +++ b/docs/install.md @@ -80,7 +80,6 @@ git clone https://github.com/DendrouLab/panpipes cd panpipes pip install . ``` -Now skip to [step 3](#step-3-pipeline-configuration) ### Option 2: python venv environment: @@ -131,6 +130,9 @@ 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, jump to [step 3](#step-3-pipeline-configuration) + ## Step 3 pipeline configuration