From 5a79d545593b83e453eb12bbaef40c9d206197e6 Mon Sep 17 00:00:00 2001
From: subwaystation <simon.heumos@qbic.uni-tuebingen.de>
Date: Tue, 10 Jan 2023 10:45:55 +0100
Subject: [PATCH] update docs

---
 README.md                 | 4 ++--
 docs/rst/installation.rst | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/README.md b/README.md
index 87843d7..af7da23 100644
--- a/README.md
+++ b/README.md
@@ -248,7 +248,7 @@ cd pggb
 you can run the container using the [human leukocyte antigen (HLA) data](data/HLA) provided in this repo:
 
 ```bash
-docker run -it -v ${PWD}/data/:/data ghcr.io/pangenome/pggb:latest "pggb -i /data/HLA/DRB1-3123.fa.gz -p 70 -s 3000 -G 2000 -n 10 -t 16 -v -V 'gi|568815561:#' -o /data/out -M -m"
+docker run -it -v ${PWD}/data/:/data ghcr.io/pangenome/pggb:latest /bin/bash -c "pggb -i /data/HLA/DRB1-3123.fa.gz -p 70 -s 3000 -G 2000 -n 10 -t 16 -v -V 'gi|568815561:#' -o /data/out -M -m"
 ```
 
 The `-v` argument of `docker run` always expects a full path.
@@ -277,7 +277,7 @@ docker build --target binary -t ${USER}/pggb:latest .
 Staying in the `pggb` directory, we can run `pggb` with the locally built image:
 
 ```bash
-docker run -it -v ${PWD}/data/:/data ${USER}/pggb "pggb -i /data/HLA/DRB1-3123.fa.gz -p 70 -s 3000 -G 2000 -n 10 -t 16 -v -V 'gi|568815561:#' -o /data/out -M -m"
+docker run -it -v ${PWD}/data/:/data ${USER}/pggb /bin/bash -c "pggb -i /data/HLA/DRB1-3123.fa.gz -p 70 -s 3000 -G 2000 -n 10 -t 16 -v -V 'gi|568815561:#' -o /data/out -M -m"
 ```
 A script that handles the whole building process automatically can be found at https://github.com/nf-core/pangenome#building-a-native-container.
 
diff --git a/docs/rst/installation.rst b/docs/rst/installation.rst
index 7c833d1..283fe7e 100644
--- a/docs/rst/installation.rst
+++ b/docs/rst/installation.rst
@@ -56,7 +56,7 @@ you can run the container using the human leukocyte antigen (HLA) data provided
 
 .. code-block:: bash
 
-    docker run -it -v ${PWD}/data/:/data ghcr.io/pangenome/pggb:latest "pggb -i /data/HLA/DRB1-3123.fa.gz -p 70 -s 3000 -G 2000 -n 10 -t 16 -v -V 'gi|568815561:#' -o /data/out -M -C cons,100,1000,10000 -m"
+    docker run -it -v ${PWD}/data/:/data ghcr.io/pangenome/pggb:latest /bin/bash -c "pggb -i /data/HLA/DRB1-3123.fa.gz -p 70 -s 3000 -G 2000 -n 10 -t 16 -v -V 'gi|568815561:#' -o /data/out -M -C cons,100,1000,10000 -m"
 
 
 The ``-v`` argument of ``docker run`` always expects a full path.
@@ -93,7 +93,7 @@ Staying in the ``pggb`` directory, we can run ``pggb`` with the locally build im
 
 .. code-block:: bash
 
-    docker run -it -v ${PWD}/data/:/data ${USER}/pggb "pggb -i /data/HLA/DRB1-3123.fa.gz -p 70 -s 3000 -G 2000 -n 10 -t 16 -v -V 'gi|568815561:#' -o /data/out -M -C cons,100,1000,10000 -m"
+    docker run -it -v ${PWD}/data/:/data ${USER}/pggb /bin/bash -c "pggb -i /data/HLA/DRB1-3123.fa.gz -p 70 -s 3000 -G 2000 -n 10 -t 16 -v -V 'gi|568815561:#' -o /data/out -M -C cons,100,1000,10000 -m"
 
 A script that handles the whole building process automatically can be found at `https://github.com/nf-core/pangenome#building-a-native-container <https://github.com/nf-core/pangenome#building-a-native-container>`_`.