malariagen / ag1000g-phase1-vgsc-report

MIT License
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Fix install #171

Closed alimanfoo closed 6 years ago

alimanfoo commented 6 years ago

This PR updates the agam-report-base submodule which brings in some fixes for a broken texlive installation script.

alimanfoo commented 6 years ago

Hi @cclarkson, I've updated the agam-report-base submodule, which should bring in some updated install scripts for miniconda and texlive. To rebuild dependencies, from a local clone of your fork, do:

git checkout master
git fetch upstream
git rebase upstream/master
git submodule update
rm -rf deps
./agam-report-base/install/install-conda.sh
./agam-report-base/install/install-texlive.sh

It will take a while. If you're feeling impatient, you can run install-conda.sh and install-texlive.sh at the same time in separate terminals.

If you have any working branches, probably helpful to also rebase them on upstream master, e.g.:

git checkout my-working-branch
git rebase upstream/master
git push -f origin my-working-branch
alimanfoo commented 6 years ago

@cclarkson sorry, forgot an important command when rebasing your master...

git checkout master
git fetch upstream
git rebase upstream/master
git submodule update
# forgot this
git push -f origin master