[fixup] quick install

Author: DrYak

.github/workflows/tutorials.yaml

@@ -60,6 +60,7 @@ jobs:
         # run: ./convert.sh --branch *_install.md
         run: |
           mkdir -p _test_tutorials
+          ./convert.sh --version --branch --sralog --patch_only documentation/*.md tutorials/*.md
           python extract_bash_code.py -o _test_tutorials documentation/*.md tutorials/*.md
           cd _test_tutorials
           bash installation.sh

docs/convert.sh

@@ -1,5 +1,6 @@
 #!/usr/bin/env bash
 
+patch_only=0
 patch_branch=0
 version=0
 patch_sralog=0
@@ -17,6 +18,9 @@ while [[ -n $1 ]]; do
 		--sralog|sralog)
 			patch_sralog=1
 		;;
+		--patch-only|--patchonly|patchonly|patch-only)
+			patch_only=1
+		;;
 		--dryrun|--dry-run|dryrun|dry-run)
 			dryrun=1
 		;;
@@ -76,6 +80,11 @@ if (( patch_sralog )); then
 	sed -ri 's@fasterq-dump --progress.*$@\0 2> >(tee download.err.log >\&2)@g' "${alltut[@]}"
 fi
 
+if (( patch_only )); then
+	echo "Only patching. You can run the tutorials yourself"
+	exit 0
+fi
+
 execute='--execute'
 if (( dryrun )); then
 	execute=''

docs/documentation/installation.md

@@ -25,7 +25,7 @@ The present tutorial will show you how to install V-pipe and the dependencies re
 Download the install script and run it with the following parameters:
 
 ```bash
-curl -O 'https://raw.githubusercontent.com/GeertvanGeest/V-pipe/refs/heads/gsod-rtd/utils/quick_install.sh'
+curl -O 'https://raw.githubusercontent.com/cbg-ethz/V-pipe/master/utils/quick_install.sh'
 bash quick_install.sh -p vp-analysis -w work
 
 ```
@@ -41,7 +41,7 @@ V-pipe uses the [Bioconda](https://bioconda.github.io/) bioinformatics software
 
 ```bash
 ## not run
-curl -O 'https://raw.githubusercontent.com/GeertvanGeest/V-pipe/refs/heads/gsod-rtd/utils/quick_install.sh'
+curl -O 'https://raw.githubusercontent.com/cbg-ethz/V-pipe/master/utils/quick_install.sh'
 bash quick_install.sh -p vp-analysis -w work
 ```
 

utils/quick_install.sh

@@ -3,8 +3,8 @@
 # defaults
 PREFIX=$(pwd)
 FORCE=
-REPO=https://github.com/GeertvanGeest/V-pipe.git
-BRANCH=gsod-rtd
+REPO=https://github.com/cbg-ethz/V-pipe.git
+BRANCH=master
 RELEASE=
 WORKDIR=
 MINIMAL=