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fix: redirect HOME to /tmp in Nextflow env so ChimeraX can write its data dir #104

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Merged
St3451 merged 3 commits into from
May 28, 2026
Merged

fix: redirect HOME to /tmp in Nextflow env so ChimeraX can write its data dir #104

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45bc431
fix: redirect HOME to /tmp so ChimeraX can write its data dir under S…
St3451 May 28, 2026
6f78244
fix: clarify comment on HOME redirection for ChimeraX in Singularity
St3451 May 28, 2026
66679cb
fix: update HOME variable handling for ChimeraX in Singularity
St3451 May 28, 2026
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6 changes: 6 additions & 0 deletions oncodrive3d_pipeline/modules/o3d_chimerax_plot.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -15,6 +15,12 @@ process O3D_CHIMERAX_PLOT {
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${cohort}"
"""
# Give ChimeraX a writable, per-task HOME so it can initialise its data
# directory (\$HOME/.chimerax) without colliding with concurrent tasks or
# hitting a read-only host \$HOME inside Singularity.
export HOME="\$PWD/.chimerax-home"
mkdir -p "\$HOME"
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oncodrive3D chimerax-plot \\
-o $prefix \\
-g $genes_csv \\
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