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Merge pull request #220 from Australian-Structural-Biology-Computing/…
…add-rosettafold-all-atom Add RoseTTAFold-All-Atom
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,39 @@ | ||
| /* | ||
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
| Config file for defining DSL2 per module options and publishing paths | ||
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
| Available keys to override module options: | ||
| ext.args = Additional arguments appended to command in module. | ||
| ext.args2 = Second set of arguments appended to command in module (multi-tool modules). | ||
| ext.args3 = Third set of arguments appended to command in module (multi-tool modules). | ||
| ext.prefix = File name prefix for output files. | ||
| ---------------------------------------------------------------------------------------- | ||
| */ | ||
|
|
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| process { | ||
| withName: 'GUNZIP|ARIA2_PDB_SEQRES' { | ||
| publishDir = [ | ||
| path: {"${params.outdir}/DBs/rosettafold_all_atom/"}, | ||
| mode: 'symlink', | ||
| saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, | ||
| ] | ||
| } | ||
|
|
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| withName: 'RUN_ROSETTAFOLD_ALL_ATOM' { | ||
| if(params.use_gpu) { accelerator = 1 } | ||
| publishDir = [ | ||
| path: { "${params.outdir}/rosettafold_all_atom/" }, | ||
| mode: 'copy', | ||
| saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, | ||
| pattern: '*.*' | ||
| ] | ||
| } | ||
|
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| withName: 'NFCORE_PROTEINFOLD:ROSETTAFOLD_ALL_ATOM:MULTIQC' { | ||
| publishDir = [ | ||
| path: { "${params.outdir}/multiqc" }, | ||
| mode: 'copy', | ||
| saveAs: { filename -> filename.equals('versions.yml') ? null : "rosettafold_all_atom_$filename" } | ||
| ] | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,36 @@ | ||
| /* | ||
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
| Nextflow config file for running minimal tests | ||
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
| Defines input files and everything required to run a fast and simple pipeline test. | ||
| Use as follows: | ||
| nextflow run nf-core/proteinfold -profile test_rosettafold_all_atom,<docker/singularity> --outdir <OUTDIR> | ||
| ---------------------------------------------------------------------------------------- | ||
| */ | ||
|
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| stubRun = true | ||
|
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| // Limit resources so that this can run on GitHub Actions | ||
| process { | ||
| resourceLimits = [ | ||
| cpus: 4, | ||
| memory: '15.GB', | ||
| time: '1.h' | ||
| ] | ||
| } | ||
|
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| params { | ||
| config_profile_name = 'Test profile' | ||
| config_profile_description = 'Minimal test dataset to check pipeline function' | ||
|
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| // Input data to test rosettafold_all_atom | ||
| mode = 'rosettafold_all_atom' | ||
| rosettafold_all_atom_db = "${projectDir}/assets/dummy_db_dir" | ||
| input = params.pipelines_testdata_base_path + 'proteinfold/testdata/samplesheet/v1.2/samplesheet.csv' | ||
| } | ||
|
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| process { | ||
| withName: 'RUN_ROSETTAFOLD_ALL_ATOM' { | ||
| container = 'biocontainers/gawk:5.1.0' | ||
| } | ||
| } |
35 changes: 35 additions & 0 deletions
35
dockerfiles/Dockerfile_nfcore-proteinfold_rosettafold_all_atom
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,35 @@ | ||
| FROM nvidia/cuda:12.6.0-cudnn-devel-ubuntu24.04 | ||
|
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| LABEL Author="[email protected]" \ | ||
| title="nfcore/proteinfold_rosettafold_all_atom" \ | ||
| Version="1.2.0dev" \ | ||
| description="Docker image containing all software requirements to run the RUN_ROSETTAFOLD_ALL_ATOM module using the nf-core/proteinfold pipeline" | ||
|
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| ENV PYTHONPATH="/app/RoseTTAFold-All-Atom" \ | ||
| PATH="/conda/bin:/app/RoseTTAFold-All-Atom:$PATH" \ | ||
| DGLBACKEND="pytorch" \ | ||
| LD_LIBRARY_PATH="/conda/lib:/usr/local/cuda-12.6/lib64:$LD_LIBRARY_PATH" | ||
|
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| RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y wget git && \ | ||
| wget -q -P /tmp "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh" && \ | ||
| bash /tmp/Miniforge3-$(uname)-$(uname -m).sh -b -p /conda && \ | ||
| rm -rf /tmp/Miniforge3-$(uname)-$(uname -m).sh /var/lib/apt/lists/* && \ | ||
| apt-get autoremove -y && apt-get clean -y | ||
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| RUN git clone --single-branch --depth 1 https://github.com/Australian-Structural-Biology-Computing/RoseTTAFold-All-Atom.git /app/RoseTTAFold-All-Atom && \ | ||
| cd /app/RoseTTAFold-All-Atom && \ | ||
| /conda/bin/mamba env create --file=environment.yaml && \ | ||
| /conda/bin/mamba run -n RFAA bash -c \ | ||
| "python /app/RoseTTAFold-All-Atom/rf2aa/SE3Transformer/setup.py install && \ | ||
| bash /app/RoseTTAFold-All-Atom/install_dependencies.sh" && \ | ||
| /conda/bin/mamba clean --all --force-pkgs-dirs -y | ||
|
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| RUN cd /app/RoseTTAFold-All-Atom && \ | ||
| wget https://ftp.ncbi.nlm.nih.gov/blast/executables/legacy.NOTSUPPORTED/2.2.26/blast-2.2.26-x64-linux.tar.gz && \ | ||
| mkdir -p blast-2.2.26 && \ | ||
| tar -xf blast-2.2.26-x64-linux.tar.gz -C blast-2.2.26 && \ | ||
| cp -r blast-2.2.26/blast-2.2.26/ blast-2.2.26_bk && \ | ||
| rm -r blast-2.2.26 && \ | ||
| mv blast-2.2.26_bk/ blast-2.2.26 && \ | ||
| rm -rf /root/.cache *.tar.gz && \ | ||
| apt-get autoremove -y && apt-get remove --purge -y wget git && apt-get clean -y |
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