git clone --recursive https://github.com/trinityrnaseq/trinityrnaseq.git

#############################

Release info:

curl https://api.github.com/repos/trinityrnaseq/trinityrnaseq/releases


## master upgrade to latest devel:

git pull origin devel
git submodule foreach --recursive git checkout master
git submodule foreach --recursive git pull
git submodule foreach --recursive git submodule init 
git submodule foreach --recursive git submodule update 


#####

Checks before release:

-pombe, mouse, drosoph, k562
-make test_all
-docker: run_test_docker.sh
-singularity: run_ext_test_singularity.sh

-update version string in Trinity
-update Changelog.txt for new version release notes.


git clone --recursive https://github.com/trinityrnaseq/trinityrnaseq.git

Make 2 release tarballs, identical except the latter includes the extended test data.

make clean -i
find . -regex ".*git" -exec rm -rf {} \;

-release naming convention:
   release version tag on github: Trinity-v2.8.6
   
   -standard release (extended test data removed)
	  basedir: trinityrnaseq-v2.8.6
	  filename: trinityrnaseq-v2.8.6.FULL.tar.gz
      

   -including extended test data
      same basedir as above
	  filename: trinityrnaseq-v2.8.6.FULL_with_extendedTestData.tar.gz



singularity:
  copy the simg to gs://trinityrnaseq/Singularity/
  add to https://data.broadinstitute.org/Trinity/TRINITY_SINGULARITY/