From d015de926d1c635d98aa8cc22df545ab53e6de2c Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Mon, 3 May 2021 21:21:01 +0200
Subject: [PATCH] README formatting

---
 docker/qmean_qmeandisco_example/README.md | 2 ++
 docker/qmeanbrane_example/README.md       | 2 ++
 2 files changed, 4 insertions(+)

diff --git a/docker/qmean_qmeandisco_example/README.md b/docker/qmean_qmeandisco_example/README.md
index a2b89f8..e7fc2f2 100644
--- a/docker/qmean_qmeandisco_example/README.md
+++ b/docker/qmean_qmeandisco_example/README.md
@@ -16,7 +16,9 @@ sudo docker run --workdir $(pwd) -v $(pwd):$(pwd) -v <PATH_TO_LOCAL_UNICLUST>:/u
 The directory contains pre-computed profiles that match the 
 sequences in targets.fasta. To speed things up, you can provide them as argument:
 
+```terminal
 sudo docker run --workdir $(pwd) -v $(pwd):$(pwd) -v <PATH_TO_LOCAL_UNICLUST>:/uniclust30 registry.scicore.unibas.ch/schwede/qmean:4.2.0 run_qmean.py model.pdb --method QMEAN --seqres targets.fasta --profiles query_hhblits_one.a3m query_hhblits_two.a3m
+```
 
 Normally, the container creates a temporary directory to store intermediate 
 results. If you want to investigate them, or access the sequence profiles,
diff --git a/docker/qmeanbrane_example/README.md b/docker/qmeanbrane_example/README.md
index 5a3f482..7b263df 100644
--- a/docker/qmeanbrane_example/README.md
+++ b/docker/qmeanbrane_example/README.md
@@ -20,7 +20,9 @@ sudo docker run --workdir $(pwd) -v $(pwd):$(pwd) -v <PATH_TO_LOCAL_UNICLUST>:/u
 The directory contains an already pre-computed profile which matches the 
 sequence in targets.fasta. To speed things up, you can provide it as argument:
 
+```terminal
 sudo docker run --workdir $(pwd) -v $(pwd):$(pwd) -v <PATH_TO_LOCAL_UNICLUST>:/uniclust30 registry.scicore.unibas.ch/schwede/qmean:4.2.0 run_qmean.py original_hhblits_alignment.pdb shift_in_front_helix_four.pdb shift_into_middle.pdb shift_towards_cter.pdb --method QMEANBrane  --seqres targets.fasta --profiles query_hhblits.a3m
+```
 
 Normally, the container creates a temporary directory to store intermediate 
 results. If you want to investigate them, or access the sequence profiles,
-- 
GitLab