diff --git a/.vscode/settings.json b/.vscode/settings.json index e190e43..8d3b224 100644 --- a/.vscode/settings.json +++ b/.vscode/settings.json @@ -4,6 +4,8 @@ "chmod", "cygpath", "demux", + "fasta", + "fastas", "miseq", "mkdir", "wphl" diff --git a/clearlabs/README.md b/clearlabs/README.md index ce5df80..53b45f1 100644 --- a/clearlabs/README.md +++ b/clearlabs/README.md @@ -1,13 +1,14 @@ # ClearLabs -This script converts the FASTA tarball that is downloaded through the ClearLabs web portal into individual and a collective FASTA file using Cygwin. +This script converts the FASTA tarball that is downloaded through the ClearLabs +web portal into individual and a collective FASTA file using Cygwin. ## Usage To be run in Cygwin ```bash -$ convert-fastas.sh TARBALL +convert-fastas.sh TARBALL ``` ## Installation @@ -20,11 +21,11 @@ This script requires [Cygwin](https://cygwin.com/install.html). 3. All other default options will work 2. Open the Cygwin console and use the following commands -```bash -$ git clone https://github.com/MillironX/wphl-bioinformatics.git -$ cp wphl-bioinformatics/clearlabs/convert-fastas.sh ~ -$ chmod +x convert-fastas.sh -``` + ```bash + git clone https://github.com/MillironX/wphl-bioinformatics.git + cp wphl-bioinformatics/clearlabs/convert-fastas.sh ~ + chmod +x convert-fastas.sh + ``` 3. Press the Win+R on the keyboard 4. Type `shell:sendto` and press Enter @@ -32,9 +33,10 @@ $ chmod +x convert-fastas.sh 6. Type `C:\cygwin64\bin\bash.exe` and click Next 7. Type `Convert FASTA Tarball` or something else memorable and click Finish 8. Right-click the newly created shortcut and click Properties -9. In the Target textbox, add ` --login convert-fastas.sh` (including the space) to the existing text +9. In the Target textbox, add a space and `--login convert-fastas.sh` to the + existing text 10. Click OK -An item will now be added to the Right click | Send to menu for FASTA tarballs. Once clicked, the extracted tarballs can be found in `C:\cygwin64\home\`. - - +An item will now be added to the Right click | Send to menu for FASTA tarballs. +Once clicked, the extracted tarballs can be found in +`C:\cygwin64\home\`.