Re: [comet-ms] how to install on linux

[Jimmy Eng]

Leo,

I'll assume you didn't rename the executable in the zip file and it is named "comet.2017014.linux.exe".  Once you extract that file from the zip archive, first set its executable bit by typing

   chmod +x comet.2017014.linux.exe

Then try running Comet using:

   ./comet.2017014.linux.exe

This command should print out Comet's usage statement.  You can drop the "./" relative path reference if the current working directory (.) is set in your PATH environment variable.

To actually run a search, you need the Comet binary, a valid "comet.params" file,  and an input spectrum file.  You can type

   ./comet.2017014.linux.exe -p

to generate a file named "comet.params.new" which you will need to rename and then set proper search settings; the only setting you *need* to change in this "comet.params.new" file is the "database_name" parameter to set the FASTA database.  Let's assume your directory has "comet.2017014.linux.exe", a "comet.params", and an input file named "test.mzXML".  To run a search, type

   ./comet.2017014.linux.exe test.mzXML

If all goes well, the search will run and generate an output named "test.pep.xml".  This is obviously a very brief tutorial so give it a shot and reply back with any questions or problems.

Jimmy

On Mon, Mar 26, 2018 at 7:46 AM, Leo Hoofdman <leoho...@gmail.com> wrote:

Hi, this might be a stupid question. But how can I run comet on linux? I have downloaded comet_2017014 but how can I it in terminal? If i just type comet_2017014.linux.exe in the terminal, when I'm in the downloads folder, nothing happens. Can someone help me?