Toolset for preprocessing sequencing based traits for QTL analysis
You will need the latest version of devtools. First install the release version:
then update it to the latest developement version:
Finally you can install the latest development version of seqQTL from github with:
We use the fork & pull model for developement (based on a README from the Shogun project)
Visit the seqQTL github page and click on the Fork button. Then clone your copy of the repo and add the original seqQTL repository as upstream:
git clone [email protected]:<your id>/seqQTL.git git remote add upstream [email protected]:matthiasheinig/seqQTL.git git checkout --track origin/master
Now you're ready to work on your feature. First create a branch:
git checkout -b new_feature_name
and now you can develop your code and commit to this branch.
Once the feature is done, rebase your branch against the current upstream master:
git fetch upstream git checkout master git rebase upstream/master git checkout new_feature_name git rebase master
And now you can push into your repository:
Now go to the github website and do a pull request.
After creating a branch in your local git repository, modify the R or C++ code however you need and then run R from inside the root of the package's directory (e.g. seqQTL/) and run a few devtools commands:
library(devtools) load_all() # this should recompile the C++ code check() # does some/all of the above, as well as running R CMD check
There are a few other useful devtools commands:
install() # install the package in your R library directory document() # just rebuilds the documentation test() # just runs all tests build() # build a binary package
For more information check out the devtools site.
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