From 30b81dd9ccddbe7b5cf13217faeb1301994485ab Mon Sep 17 00:00:00 2001 From: M-casado Date: Tue, 27 Apr 2021 21:09:11 +0200 Subject: [PATCH] README modifications: installation and common issues Corrected the installation documentation from the main README, in which the repo we cloned was not the complete one (which was the desired way when we were not using the template as input). Besides, I added a new section of "common issues" when running the project in WSL2 regarding line endings. It's unrelated to the project itself, but may help others. --- Star2xml/README.md | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) 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