Commit 9bd4b674 authored by Martino Bertoni's avatar Martino Bertoni 🌋

update singularity install section

parent 23ad74f1
Pipeline #2481 passed with stages
in 10 minutes and 57 seconds
......@@ -42,17 +42,29 @@ All the dependencies for the CC will be bundled within a singularity image gener
Generating such an image requires roughly 20 minutes:
1. [Install Singularity](https://www.sylabs.io/guides/2.6/user-guide/installation.html)
1. [Install Singularity](https://sylabs.io/guides/3.8/admin-guide/admin_quickstart.html#installation-from-source)
$ sudo apt-get update && sudo apt-get install -y \
build-essential \
uuid-dev \
libgpgme-dev \
squashfs-tools \
libseccomp-dev \
wget \
pkg-config \
git \
cryptsetup-bin\
golang-go
$ export VERSION=3.8.0 && # adjust this as necessary \
wget https://github.com/sylabs/singularity/releases/download/v${VERSION}/singularity-ce-${VERSION}.tar.gz && \
tar -xzf singularity-ce-${VERSION}.tar.gz && \
cd singularity-ce-${VERSION}
$ ./mconfig && \
make -C ./builddir && \
sudo make -C ./builddir install
VER=2.5.1
wget https://github.com/sylabs/singularity/releases/download/$VER/singularity-$VER.tar.gz
tar xvf singularity-$VER.tar.gz
cd singularity-$VER
./configure --prefix=/usr/local --sysconfdir=/etc
make
sudo make install
> In case of errors during this step, check Singularity [prerequisites](https://www.sylabs.io/guides/2.6/user-guide/installation.html#before-you-begin)!
2. Clone this repository to your code folder:
......@@ -92,6 +104,14 @@ The CC rely on one config file containing the information for the current enviro
chemcheck -c /path/to/your/cc_config.json
```
## Running with alternative image
You might want to use a previously compiled or downloaded image:
```bash
chemcheck -i /path/to/your/cc_image.simg
```
## Usage
We make it trivial to either start a Jupyter Notebook within the image or to run a shell:
......
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