diff --git a/README.md b/README.md index 80ff722..fbc420f 100644 --- a/README.md +++ b/README.md @@ -14,9 +14,9 @@ There is no installation. Just clone this repository to your local machine. Make ## Building the GeneSets packages -The only thing you have to do is tell the package for which organisms you which to build annotation tables. In root of the repository, there is a file called `organisms`. Open this file with your favorite text editor and add the names of the organism(s) you want to build annotation tables for and remove any names you're not interested in. Make sure there is only one name per line and that the lines do not contain any leading or trailing white space characters. Also, make sure that the names you are using correspond exactly to the official names used by the NCBI taxonomy database, as this is the reference used by the GeneSets package. Using the correct name is especially important when working with bacterial strains and substrains. For instance, if you want to create annotation tables for Escherichia coli K12, substrain MG1655, you should write exactly: `Escherichia coli str. K-12 substr. MG1655`. When in doubt, you can look up the name of your species on the NCBI website at http://www.ncbi.nlm.nih.gov/Taxonomy/TaxIdentifier/tax_identifier.cgi and simply copy-and-paste the name into your editor. +The only thing you have to do is tell the package for which organisms you which to build annotation tables. In root of the repository, there is a file called `organisms`. Open this file with your favorite text editor and add the names of the organism(s) you want to build annotation tables for and remove any names you're not interested in. Make sure there is only one name per line and that the lines do not contain any leading or trailing white space characters. Also, make sure that the names you are using correspond exactly to the official names used by the [NCBI taxonomy database](http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi), as this is the reference used by the GeneSets package. Using the correct name is especially important when working with bacterial strains and substrains. For instance, if you want to create annotation tables for Escherichia coli K12, substrain MG1655, you should write exactly: `Escherichia coli str. K-12 substr. MG1655`. When in doubt, you can look up the name of your species on the [NCBI website]( http://www.ncbi.nlm.nih.gov/Taxonomy/TaxIdentifier/tax_identifier.cgi) and simply copy-and-paste the name into your editor. -Once you've edited the `organisms file`, you are ready to build the packages. All you have to do is open your UNIX-shell, go to the directory of the repository: +Once you've edited the `organisms` file, you are ready to build the packages. All you have to do is open your UNIX-shell, go to the directory of the repository: ``` make ```