Try the installation on a Debian system.

[malachig]

• @sakoht will take a crack at that.

[malachig]

Testing install on Debian in a sandbox. Use Debian Wheezy as this is closest to Ubuntu Precise:

mkdir wheezy_gms
cd wheezy_gms
vagrant box add debian_wheezy https://github.com/jose-lpa/packer-debian_7.6.0/releases/download/1.0/packer_virtualbox-iso_virtualbox.box
vagrant init debian_wheezy
vagrant up
vagrant ssh
cd /vagrant
sudo apt-get update
sudo apt-get install git ssh make vim byobu
git clone https://github.com/genome/gms.git
cd gms
make
sudo passwd
sudo passwd vagrant
cd /
sudo mv opt/ opt2
mkdir /vagrant/gms/opt
sudo ln -s /vagrant/gms/opt opt
sudo mv opt2/* /opt/
sudo rm -fr opt2
cd /vagrant/gms/
make

[malachig]

Using the above approach I am able to get started but quickly encounter an error when attempting to download the APT package snapshot. I can get around this by using wget instead of $(FTP) in the Makefile. The packages are downloaded, but then when I attempt to install them I encounter this cluster of broken package dependencies:

Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:

The following packages have unmet dependencies:

 genome-snapshot-deps : Depends: genome-snapshot-deps-trans-abyss (= 2014.04.02-1~Ubuntu~precise) but it is not going to be installed
                        Depends: genome-snapshot-deps-python (= 2014.04.02-1~Ubuntu~precise) but it is not going to be installed
                        Depends: genome-snapshot-deps-perl (= 2014.04.02-1~Ubuntu~precise) but it is not going to be installed
                        Depends: genome-snapshot-deps-apps-tgi (= 2014.04.02-1~Ubuntu~precise) but it is not going to be installed
                        Depends: genome-snapshot-deps-apps-external (= 2014.04.02-1~Ubuntu~precise) but it is not going to be installed
 libcairo2-dev : Depends: libfontconfig1-dev (>= 2.2.95) but it is not going to be installed
                 Depends: libfreetype6-dev (>= 2.1.10) but it is not going to be installed
                 Depends: libx11-dev but it is not going to be installed
                 Depends: libxrender-dev (>= 0.6) but it is not going to be installed
                 Depends: libxcb1-dev (>= 1.4) but it is not going to be installed
                 Depends: libxcb-render0-dev (>= 0.9.92) but it is not going to be installed
                 Depends: libxcb-shm0-dev but it is not going to be installed
                 Depends: libglib2.0-dev but it is not going to be installed
 libglu1-mesa-dev : Depends: libgl1-mesa-dev or
                             libgl1-mesa-dev-lts-quantal but it is not going to be installed or
                             libgl1-mesa-dev-lts-raring but it is not going to be installed or
                             libgl1-mesa-dev-lts-saucy but it is not going to be installed or
                             libgl1-mesa-dev-lts-trusty but it is not going to be installed or
                             libgl-dev
 libhdf5-serial-dev : Depends: libhdf5-serial-1.8.4 (= 1.8.4-patch1-3ubuntu2) but it is not going to be installed
 mailutils : Depends: libmailutils2 (> 1:2.1) but it is not going to be installed
 postgresql : Depends: postgresql-9.1 but it is not going to be installed
 sqlite3 : Depends: libsqlite3-0 (= 3.7.9-2ubuntu1.1) but 3.7.13-1+deb7u1 is to be installed
 tk-dev : Depends: tk8.5-dev (>= 8.5.0-1) but it is not going to be installed
E: Unable to correct problems, you have held broken packages.
make[1]: *** [done-host/pkgs] Error 100

I suspect that it simply isn't realistic to expect such a complicated system to "just work" on an OS where we have conducted no testing. We encountered quite a few issues migrating from Ubuntu lucid to precise. Even different flavors of Ubuntu (installing from disk on dedicated hardware, installing from an Amazon AMI, installing in a Vagrant VM using their default precise64 image, etc.) all caused breaks to the installer that each required a workaround (and then testing on all the other target install environments to make sure the workaround didn't break them...)

[sakoht]

The best answer for the reviewer is to keep them away from mixing a GMS server install with other platforms on the same instance.

Possible text:

The GMS is not something you add to an existing Linux host/server. It is an appliance server that happens to be built on a Ubuntu Linux core. You should install it on its own machine, or use a VM or Docker container on an existing server. Even if you happen to run Ubuntu at the correct version I a server missing its goalsm, the GMS might upgrade things that make it incompatible with the system configuration you intend to use for other tasks. We build on Linux to make extension accessible, not to have the system run on hybrid servers.

Our recommendation is that you have the GMS talk to other systems in your organization through standard Internet protocols, including HTTP, NFS, SSH, SFTP, and database protocols. Change the GMS onky for security or to develop additional components.

On Mar 20, 2015, at 9:30 AM, Malachi Griffith [email protected] wrote:

Using the above approach I am able to get started but quickly encounter an error when attempting to download the APT package snapshot. I can get around this by using wget instead of $(FTP) in the Makefile. The packages are downloaded, but then when I attempt to install them I encounter this cluster of broken package dependencies:

Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:

The following packages have unmet dependencies:

genome-snapshot-deps : Depends: genome-snapshot-deps-trans-abyss (= 2014.04.02-1Ubuntuprecise) but it is not going to be installed
Depends: genome-snapshot-deps-python (= 2014.04.02-1Ubuntuprecise) but it is not going to be installed
Depends: genome-snapshot-deps-perl (= 2014.04.02-1Ubuntuprecise) but it is not going to be installed
Depends: genome-snapshot-deps-apps-tgi (= 2014.04.02-1Ubuntuprecise) but it is not going to be installed
Depends: genome-snapshot-deps-apps-external (= 2014.04.02-1Ubuntuprecise) but it is not going to be installed
libcairo2-dev : Depends: libfontconfig1-dev (>= 2.2.95) but it is not going to be installed
Depends: libfreetype6-dev (>= 2.1.10) but it is not going to be installed
Depends: libx11-dev but it is not going to be installed
Depends: libxrender-dev (>= 0.6) but it is not going to be installed
Depends: libxcb1-dev (>= 1.4) but it is not going to be installed
Depends: libxcb-render0-dev (>= 0.9.92) but it is not going to be installed
Depends: libxcb-shm0-dev but it is not going to be installed
Depends: libglib2.0-dev but it is not going to be installed
libglu1-mesa-dev : Depends: libgl1-mesa-dev or
libgl1-mesa-dev-lts-quantal but it is not going to be installed or
libgl1-mesa-dev-lts-raring but it is not going to be installed or
libgl1-mesa-dev-lts-saucy but it is not going to be installed or
libgl1-mesa-dev-lts-trusty but it is not going to be installed or
libgl-dev
libhdf5-serial-dev : Depends: libhdf5-serial-1.8.4 (= 1.8.4-patch1-3ubuntu2) but it is not going to be installed
mailutils : Depends: libmailutils2 (> 1:2.1) but it is not going to be installed
postgresql : Depends: postgresql-9.1 but it is not going to be installed
sqlite3 : Depends: libsqlite3-0 (= 3.7.9-2ubuntu1.1) but 3.7.13-1+deb7u1 is to be installed
tk-dev : Depends: tk8.5-dev (>= 8.5.0-1) but it is not going to be installed
E: Unable to correct problems, you have held broken packages.
make[1]: *** [done-host/pkgs] Error 100
I suspect that it simply isn't realistic to expect such a complicated system to "just work" on an OS where we have conducted no testing. We encountered quite a few issues migrating from Ubuntu lucid to precise. Even different flavors of Ubuntu (installing from disk on dedicated hardware, installing from an Amazon AMI, installing in a Vagrant VM using their default precise64 image, etc.) all caused breaks to the installer that each required a workaround (and then testing on all the other target install environments to make sure the workaround didn't break them...)

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