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modify installation #105

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Sep 17, 2023
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modify installation #105

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modify installation
bio-la Sep 17, 2023
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bio-la Sep 17, 2023
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48 changes: 29 additions & 19 deletions docs/install.md
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Original file line number Diff line number Diff line change
@@ -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

Expand Down Expand Up @@ -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
Expand All @@ -72,7 +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:

Expand Down Expand Up @@ -123,6 +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

Expand Down