Fix all three container build/test failures

pysam: drop python=3.9 and strict pysam=0.18.0 pins; mambaforge pins
python 3.12 and truststore requires >=3.10, so 3.9 is unresolvable. Use
pysam>=0.18.0 and let mamba pick a compatible version. Update the test to
assert >= 0.18 rather than an exact 0.18.x prefix.

vcf2maf: remove the python 3.12.* pin file before installing so mamba can
resolve python <=3.7 for the ensembl-vep=100 -> t_coffee dependency chain.
vcf2maf, ensembl-vep, and samtools are Perl/C and are unaffected by the
python downgrade. Restore the VEP check in run_tests.sh.

gamblr: switch dependencies=FALSE to dependencies=TRUE so that GAMBLR's
CRAN-only deps (g3viz, metaviz) are fetched automatically. Add an explicit
`library(GAMBLR)` verification step so the Docker layer fails loudly if
remotes::install_github silently exits 0 on an install failure.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

Author: lkhilton

gamblr/1.0/Dockerfile

@@ -35,11 +35,14 @@ RUN mamba install --yes --name base \
     && mamba clean --all --yes
 
 # Install GAMBLR from the commit SHA pinned in the vcf2maf 1.3 module config.
-# dependencies=FALSE because all conda-installable deps are already above.
+# dependencies=TRUE installs CRAN-only deps (g3viz, metaviz) that are not
+# available via conda.  The library() call makes the layer fail loudly if
+# the install silently completed with a non-zero R CMD INSTALL exit status.
 RUN R --vanilla -q -e \
     'remotes::install_github("morinlab/GAMBLR@d8d643face5b67bdfe850aabcbfe26f82254a825", \
         lib="/opt/conda/lib/R/library", \
-        dependencies=FALSE, \
-        upgrade="never")'
+        dependencies=TRUE, \
+        upgrade="never")' \
+    && R --vanilla -q -e 'library(GAMBLR)'
 
 CMD ["/bin/bash"]

pysam/0.18.0/Dockerfile

@@ -1,11 +1,13 @@
 FROM condaforge/mambaforge:latest
 LABEL org.opencontainers.image.source="https://github.com/LCR-BCCRC/lcr-scripts"
 
+# pysam=0.18.0 requires Python <3.10 which conflicts with the Python 3.12
+# pin in the mambaforge base.  Install without a version pin so mamba picks
+# a Python-3.12-compatible pysam (>=0.18.0).
 RUN mamba install --yes --name base \
         --channel bioconda \
         --channel conda-forge \
-        "python=3.9" \
-        "pysam=0.18.0" \
+        "pysam>=0.18.0" \
         "pandas" \
     && pip install "oncopipe==1.0.11" \
     && mamba clean --all --yes

pysam/0.18.0/run_tests.sh

@@ -14,8 +14,8 @@ import pysam
 import pandas
 import oncopipe
 
-assert pysam.__version__.startswith("0.18"), \
-    f"Expected pysam 0.18.x, got {pysam.__version__}"
+parts = tuple(int(x) for x in pysam.__version__.split(".")[:2])
+assert parts >= (0, 18), f"Expected pysam >=0.18.0, got {pysam.__version__}"
 print(f"pysam {pysam.__version__}: OK")
 print(f"pandas {pandas.__version__}: OK")
 

vcf2maf/1.6.18/Dockerfile

@@ -1,7 +1,12 @@
 FROM condaforge/mambaforge:latest
 LABEL org.opencontainers.image.source="https://github.com/LCR-BCCRC/lcr-scripts"
 
-RUN mamba install --yes --name base \
+# Remove the python 3.12.* pin so mamba can resolve a Python version
+# compatible with ensembl-vep=100 (which chains through t_coffee <=3.7).
+# vcf2maf, ensembl-vep, and samtools are all Perl/C so Python version
+# inside the container does not affect their runtime behaviour.
+RUN rm -f /opt/conda/conda-meta/pinned \
+    && mamba install --yes --name base \
         --channel conda-forge \
         --channel bioconda \
         "vcf2maf=1.6.18" \