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Fix HOME env for colabfold weight download, increase resources, use v3 tag

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Olamide Isreal
2026-03-26 17:46:41 +01:00
parent 844d34c04a
commit 4cd23d549b
3 changed files with 11 additions and 6 deletions
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4
Dockerfile.wes
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@@ -14,6 +14,10 @@ RUN python3 -m pip install --upgrade pip && \
# Add user entry for UID 1000 (k8s default) to avoid getpwuid errors # Add user entry for UID 1000 (k8s default) to avoid getpwuid errors
RUN useradd -u 1000 -m -s /bin/bash nextflow || true RUN useradd -u 1000 -m -s /bin/bash nextflow || true
# Set HOME for UID 1000 so colabfold weights download to writable location
ENV HOME=/home/nextflow
RUN mkdir -p /home/nextflow/.cache && chmod -R 777 /home/nextflow
RUN mkdir -p /opt/bioemu/scripts/ /data /results && chmod -R 777 /data /results RUN mkdir -p /opt/bioemu/scripts/ /data /results && chmod -R 777 /data /results
COPY calculate_gibbs.py /opt/bioemu/scripts/ COPY calculate_gibbs.py /opt/bioemu/scripts/

6
main.nf
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@@ -13,7 +13,7 @@ params.temperature = 300
params.n_clusters = 5 params.n_clusters = 5
process GENERATE_STRUCTURE_1 { process GENERATE_STRUCTURE_1 {
container 'harbor.cluster.omic.ai/omic/bioemu:v2' container 'harbor.cluster.omic.ai/omic/bioemu:v3'
publishDir "${params.outdir}/${params.complex_name}/protein1", mode: 'copy' publishDir "${params.outdir}/${params.complex_name}/protein1", mode: 'copy'
input: input:
@@ -41,7 +41,7 @@ process GENERATE_STRUCTURE_1 {
} }
process GENERATE_STRUCTURE_2 { process GENERATE_STRUCTURE_2 {
container 'harbor.cluster.omic.ai/omic/bioemu:v2' container 'harbor.cluster.omic.ai/omic/bioemu:v3'
publishDir "${params.outdir}/${params.complex_name}/protein2", mode: 'copy' publishDir "${params.outdir}/${params.complex_name}/protein2", mode: 'copy'
input: input:
@@ -69,7 +69,7 @@ process GENERATE_STRUCTURE_2 {
} }
process CALCULATE_BINDING { process CALCULATE_BINDING {
container 'harbor.cluster.omic.ai/omic/bioemu:v2' container 'harbor.cluster.omic.ai/omic/bioemu:v3'
publishDir "${params.outdir}/${params.complex_name}/analysis", mode: 'copy' publishDir "${params.outdir}/${params.complex_name}/analysis", mode: 'copy'
input: input:

7
nextflow.config
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@@ -11,9 +11,10 @@ docker {
} }
process { process {
container = 'harbor.cluster.omic.ai/omic/bioemu:v2' container = 'harbor.cluster.omic.ai/omic/bioemu:v3'
cpus = 2 cpus = 4
memory = '8 GB' memory = '16 GB'
time = '2h'
} }
profiles { profiles {