BamLiquidator Packaging

Overview

• make dput needs to be run from a proper environment to update the bamliquidator ppa version
  • prerequisites in addition to developer setup on Ubuntu 18.04: sudo apt install devscripts python-all python-stdeb dput
• the Bradner Lab main EC2 instance is configured for packaging with the user packager
  • you can use the ubuntu ssh key to as packager
  • if you need the gpg passphrase, contact jdimatteo@gmail.com
• Ubuntu Launchpad account name is dfbradnerlab@gmail.com
  • Upload errors and acknowledgments are emailed to dfbradnerlab@gmail.com
• it takes a few minutes for new versions to be published
  • it takes a couple minutes for the upload acknowledgment to be emailed
  • next, it takes a couple more minutes to go from status "Pending" to "Published" at https://launchpad.net/~bradner-computation/+archive/ubuntu/pipeline/+packages

Example Updating the Package Version

$ ssh packager@ec2
$ cd pipeline/bamliquidator_internal/
$ git pull
$ make dput

Example Testing Package Before Uploading

$ ssh packager@ec2
$ cd pipeline/bamliquidator_internal/
$ git pull
$ make deb
$ scp deb_dist/python-bamliquidatorbatch_*trusty*.deb bamliquidator_*trusty*.deb ubuntu@some-other-ec2-machine:/home/ubuntu

$ ssh ubuntu@some-other-ec2-machine
$ sudo apt-get install gdebi-core
$ sudo gdebi python-bamliquidatorbatch*.deb
$ sudo gdebi bamliquidator*.deb
$ # do testing
$ sudo dpkg --remove bamliquidator python-bamliquidatorbatch

Environment Setup Notes

1. Follow the steps on https://github.com/BradnerLab/pipeline/wiki/bamliquidator#check-list
2. sudo apt-get install devscripts debhelper gnupg-agent pinentry-curses python-stdeb python-all-dev
3. generate a gpg key, e.g. gpg --gen-key
4. register the gpg key, e.g. see https://help.ubuntu.com/community/GnuPrivacyGuardHowto#Uploading_the_key_to_Ubuntu_keyserver
5. import the gpg key at https://launchpad.net/~bradner-computation/+editpgpkeys
   • you will get an email "Launchpad: Confirm your OpenPGP Key"
   • copy from "-----BEGIN PGP MESSAGE-----" to "-----END PGP MESSAGE-----" (including the BEGIN/END PGP MESSAGE lines) to a file doc.encrypted on the system with the gpg key
   • run gpg --decrypt doc.encrypted and enter your passphrase when prompted
   • follow the instructions in the decrypted message
6. to reduce number of times entering the gpg passphrase, configure gpg-agent (e.g. see http://unix.stackexchange.com/questions/46960/how-to-configure-gpg-to-enter-passphrase-only-once-per-session)