diff --git a/Star2xml/README.md b/Star2xml/README.md index 10682791..91a6f377 100644 --- a/Star2xml/README.md +++ b/Star2xml/README.md @@ -45,7 +45,8 @@ You may want to install the latest versions of this packages and check if it wor To install Python dependencies: ```bash # Step 1. Cloning the tools repository -git clone https://github.com/EbiEga/ega-metadata-schema/star2xml +git clone git@github.com:EbiEga/ega-metadata-schema.git +cd ega-metadata-schema/Star2xml/ # Step 2. Creating and activating the virtual environment virtualenv -p python3 venv_star2xml source venv_star2xml/bin/activate @@ -227,4 +228,10 @@ If the metadata requirements change and existing fields need to be removed or ne * Not using the option `--download_xsd` the first time you try to validate XMLs: the schemas (`.xsd`) will be missing and the tool will throw the following error message: ``` Bash ERROR in check_xml_is_valid(): the schema file 'downloaded_schemasXSD/SRA.sample.xsd' could not be accessed. If you have not downloaded the schema files (.xsd) yet, use '--download_xsd' when running the command. +``` +* Line endings being an issue: when using different operating systems (e.g. using Windows Subsystem for Linux) an issue regarding line endings may arise when trying to execute the scripts (_e.g._ `/usr/bin/env: ‘python3\r’: No such file or directory` - notice the `/r` not being handled correctly by the interpreter). If such is the case, there are automatic ways to change all line endings within the scripts, which will solve the issue: +``` bash +sudo apt install dos2unix +# Within the 'Star2xml/' folder do: +dos2unix ./*.py ``` \ No newline at end of file