Install Issues

[allisonheath]

Hi - thanks for putting this together, I'm trying to install it on a vanilla Ubuntu 12.04 VM. I did seem to have to install a few perl modules manually, but after that I get to the final tests and they seem to fail: https://gist.github.com/allisonheath/9531547

Ideas?

[keiranmraine]

Hi,

Can you tell me which version of the code you ran. I'm waiting on confirmation that the 'master' is working before I tag a release with various fixes.

The log suggests that all of the C-programs failed to install. You shouldn't have had to install the perl modules though that's what setup.sh is for (see INSTALL)

Brian mentioned some packages were required for successful install of the C programs but if setup.sh is used it would have failed before it hit the perl code:

``

• dh-autoreconf
• pkg-config
• ncurses-hexedit
• libncurses-dev
• libfile-sharedir-perl
  ``

[allisonheath]

Ah, I just cloned the repo :) Should I hold off until the next release?

I did run setup.sh /opt/ICGC and it appears all of the binaries were successfully installed in /opt/ICGC/bin. The only other package I needed was libtool.

Trying from scratch with v0.1.2 (and same from the head) seems the first error is Module::Build is too old:
Building BioPerl-1.006923 ... Module::Build version 0.42 required--this is only version 0.38 at ./Build line 43.

After manually upgrading, there does continue to be missing modules, e.g.: https://gist.github.com/allisonheath/9531547#file-missing-modules

[keiranmraine]

Thanks, I can add these to the dependencies, can you tell me what the perl version is on this Ubuntu build. clone is fine until the next release, it works apart from these issues you've identified.

[allisonheath]

It's perl v5.14.2. I did a full fresh install on a new VM from the repo and made a list of missing dependencies I encountered here: https://gist.github.com/allisonheath/9537011

I got to the tests and they failed slightly differently this time, also in that gist. biobambam, bwa, io_lib, libmaus, samtools and snappy all appear to have installed fine.