Installing igvxml.0.0.6 fails in test example

[julia326]

I ran a slightly modified test example:

source configuration.env
KETREW_CONFIGURATION=_kclient_config/configuration.ml; DREAM=https://storage.googleapis.com/dream-challenge; ocaml run_pipeline.ml pipeline \
       --normal $DREAM/synthetic.challenge.set2.normal.bam \
       --tumor $DREAM/synthetic.challenge.set2.tumor.bam \
       --reference-build hg38 \
       --mouse-run \
       --with-mutect2 \
       --results-path $BIOKEPI_WORK_DIR/results/ \
       -E My-first-epidisco-party

Logs from failing IGV install node:

### Kube-Job 836dc063-5db6-51b1-9368-cdfe2b6b5d2e
### Freshness: Fresh
### Output:

User
biokepi
Host
836dc063-5db6-51b1-9368-cdfe2b6b5d2e
Machine
Linux 836dc063-5db6-51b1-9368-cdfe2b6b5d2e 3.16.0-4-amd64 #1 SMP Debian 3.16.36-1+deb8u2 (2016-10-19) x86_64 x86_64 x86_64 GNU/Linux
biokepi
biokepi
Does not need Conda
OPAM has already been initialized.
In normal operation, OPAM only alters files within ~/.opam.

During this initialisation, you can allow OPAM to add information to two
other files for best results. You can also make these additions manually
if you wish.

If you agree, OPAM will modify:

  - ~/.profile (or a file you specify) to set the right environment
    variables and to load the auto-completion scripts for your shell (sh)
    on startup. Specifically, it checks for and appends the following line:

    .
/nfs-pool/biokepi/toolkit/biopam-kit/opam_dir/opam-root-root-igvxml.0.0.6/opam-init/init.sh
> /dev/null 2> /dev/null || true


  - ~/.ocamlinit to ensure that non-system installations of `ocamlfind`
    (i.e. those installed by OPAM) will work correctly when running the
    OCaml toplevel. It does this by adding $OCAML_TOPLEVEL_PATH to the list
    of include directories.

If you choose to not configure your system now, you can either configure
OPAM manually (instructions will be displayed) or launch the automatic setup
later by running:

   opam config setup -a


Do you want OPAM to modify ~/.profile and ~/.ocamlinit?
(default is 'no', use 'f' to name a file other than ~/.profile)
    [N/y/f] 
Global configuration:
# opam-version    1.2.2
# os              linux
File /nfs-pool/biokepi/toolkit/biopam-kit/opam_dir/opam-root-root-igvxml.0.0.6/compilers/4.02.3/4.02.3/4.02.3.comp does not exist

[smondet]

One thing I notice is that the installation does not clean-up on failure:
https://github.com/hammerlab/biokepi/blob/master/src/environment_setup/biopam.ml#L230
That would explain the OPAM has already been initialized message.