From 60597a6119ad1ac9cab9cd4c7788f6c87a809fb4 Mon Sep 17 00:00:00 2001
From: BIOPZ-Herrmann Christina <christina.herrmann@unibas.ch>
Date: Fri, 14 Feb 2020 16:45:23 +0100
Subject: [PATCH] update install instructions
- describe installation of Singularity inside `conda` environment when user has root access
- put clone repo section before install section
---
README.md | 33 +++++++++++++++++++++++++--------
1 file changed, 25 insertions(+), 8 deletions(-)
diff --git a/README.md b/README.md
index e031240..ba05bcd 100644
--- a/README.md
+++ b/README.md
@@ -14,6 +14,16 @@ workflow:
## Installation
+### Cloning the repository
+
+Traverse to the desired path on your file system, then clone the repository and
+move into it with:
+
+```bash
+git clone ssh://git@git.scicore.unibas.ch:2222/zavolan_group/pipelines/rnaseqpipeline.git
+cd rnaseqpipeline
+```
+
### Installing Singularity
For improved reproducibility and reusability of the workflow, as well as an
@@ -26,9 +36,12 @@ that Singularity be installed. See the links below for installation
instructions for the most up-to-date (as of writing) as well as for the tested
version (2.6.1) of Singularity:
+
- [Singularity v3.5](https://sylabs.io/guides/3.5/user-guide/quick_start.html)
- [Singularity v2.6](https://sylabs.io/guides/2.6/user-guide/installation.html)
+If you have root privileges, you can directly install Singularity together with snakemake in a virtual environment (see next section)
+
### Setting up a Snakemake virtual environment
In addition to Singularity, [Snakemake] needs to be installed. We strongly
@@ -43,26 +56,30 @@ minimal version (Python and package manager) [Miniconda] (see the link for
installation instructions). Be sure to select the correct version for your
operating system and ensure that you select the Python 3 option.
-To create and activate the environment, run:
+To create and activate a snakemake environment, run:
```bash
conda create -n rnaseq_pipeline \
-c bioconda \
-c conda-forge \
- snakemake=5.10.0
+ snakemake=5.10.0
conda activate rnaseq_pipeline
```
-### Cloning the repository
+or, to create a conda environment containing Snakemake AND Singularity (currently not working on MacOS):
-Traverse to the desired path on your file system, then clone the repository and
-move into it with:
+> Note: Singularity has to be installed as root, so wherever you don't have root privileges, use the installation methods described above!
```bash
-git clone ssh://git@git.scicore.unibas.ch:2222/zavolan_group/pipelines/rnaseqpipeline.git
-cd rnaseqpipeline
+conda create -n rnaseq_pipeline \
+ -c bioconda \
+ -c conda-forge \
+ snakemake=5.10.0 \
+ singularity=3.5.2
+conda activate rnaseq_pipeline
```
+
All installation requirements should now be met with.
## Testing the installation
@@ -84,7 +101,7 @@ bash tests/test_integration_workflow/test.local.sh
Execute the following command to run the test workflow on a Slurm-managed HPC.
```bash
-bash tests/test_integration_workflow/test.local.sh
+bash tests/test_integration_workflow/test.slurm.sh
```
> **NOTE:** Depending on the configuration of your Slurm installation or if
--
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