@platforma-open/milaboratories.3d-structure-prediction.software 1.0.2 → 1.0.3
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/.turbo/turbo-build.log +308 -333
- package/CHANGELOG.md +6 -0
- package/Dockerfile +7 -0
- package/dist/artifacts/py-archive/archive.json +1 -1
- package/dist/artifacts/py-docker/docker_x64.json +1 -1
- package/dist/tengo/software/immunebuilder-predict.sw.json +1 -1
- package/package.json +1 -1
- package/pkg-platforma-open-milaboratories.3d-structure-prediction.software-py-archive-1.0.3.tgz +0 -0
- package/pkg-platforma-open-milaboratories.3d-structure-prediction.software-py-archive-1.0.2.tgz +0 -0
package/.turbo/turbo-build.log
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@@ -1,6 +1,6 @@
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WARN Issue while reading "/home/runner/work/3d-structure-prediction/3d-structure-prediction/.npmrc". Failed to replace env in config: ${NPMJS_TOKEN}
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> @platforma-open/milaboratories.3d-structure-prediction.software@1.0.
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> @platforma-open/milaboratories.3d-structure-prediction.software@1.0.3 build /home/runner/work/3d-structure-prediction/3d-structure-prediction/software
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> pl-pkg build
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[32minfo[39m: Building docker images...
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#0 building with "default" instance using docker driver
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#1 [internal] load build definition from Dockerfile
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#4 docker-image://docker.io/docker/dockerfile:1@sha256:2780b5c3bab67f1f76c781860de469442999ed1a0d7992a5efdf2cffc0e3d769
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#10 22.74 Total size: 353MB
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#10 22.79 Cleaning packages..
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#10 DONE 24.7s
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#10 [2/6] RUN micromamba install -y -n base -c bioconda -c conda-forge python=3.12.10 anarci hmmer biopython=1.85 openmm=8.3.1 pdbfixer=1.12.0 numpy=2.4.3 scipy=1.17.1 && micromamba clean --all --yes
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#10 15.41 ───────────────────────────────────────────────────────────────────────────────
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#10 15.41 ───────────────────────────────────────────────────────────────────────────────
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#10 15.41 + python_abi 3.12 8_cp312 conda-forge 7kB
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#10 15.41 + tzdata 2025c hc9c84f9_1 conda-forge 119kB
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#10 15.41 + ca-certificates 2026.4.22 hbd8a1cb_0 conda-forge 131kB
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#10 15.41 + cuda-version 12.9 h4f385c5_3 conda-forge 22kB
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#10 15.41 + libzlib 1.3.2 h25fd6f3_2 conda-forge 64kB
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#10 15.41 + libgomp 15.2.0 he0feb66_18 conda-forge 603kB
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#10 15.41 + zlib 1.3.2 h25fd6f3_2 conda-forge 96kB
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#10 15.41 + zstd 1.5.7 hb78ec9c_6 conda-forge 601kB
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#10 15.41 + _openmp_mutex 4.5 20_gnu conda-forge 29kB
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#10 15.41 + ld_impl_linux-64 2.45.1 default_hbd61a6d_102 conda-forge 728kB
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#10 15.41 + libgcc 15.2.0 he0feb66_18 conda-forge 1MB
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#10 15.41 + tk 8.6.13 noxft_h366c992_103 conda-forge 3MB
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#10 15.41 + libsqlite 3.53.1 h0c1763c_0 conda-forge 955kB
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#10 15.41 + openssl 3.6.2 h35e630c_0 conda-forge 3MB
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#10 15.41 + ncurses 6.6 hdb14827_0 conda-forge 919kB
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#10 15.41 + libuuid 2.42 h5347b49_0 conda-forge 40kB
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#10 15.41 + libnsl 2.0.1 hb9d3cd8_1 conda-forge 34kB
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#10 15.41 + liblzma 5.8.3 hb03c661_0 conda-forge 113kB
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#10 15.41 + libffi 3.4.6 h2dba641_1 conda-forge 57kB
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#10 15.41 + libexpat 2.8.0 hecca717_0 conda-forge 77kB
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#10 15.41 + bzip2 1.0.8 hda65f42_9 conda-forge 260kB
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#10 15.41 + libstdcxx 15.2.0 h934c35e_18 conda-forge 6MB
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#10 15.41 + libgcc-ng 15.2.0 h69a702a_18 conda-forge 28kB
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#10 15.41 + libgfortran5 15.2.0 h68bc16d_18 conda-forge 2MB
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#10 15.41 + readline 8.3 h853b02a_0 conda-forge 345kB
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#10 15.41 + opencl-headers 2025.06.13 hecca717_0 conda-forge 56kB
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#10 15.41 + libstdcxx-ng 15.2.0 hdf11a46_18 conda-forge 28kB
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#10 15.41 + libcufft 11.4.1.4 hecca717_1 conda-forge 162MB
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#10 15.41 + cuda-nvrtc 12.9.86 hecca717_1 conda-forge 67MB
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#10 15.41 + libxcrypt 4.4.36 hd590300_1 conda-forge 100kB
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#10 15.41 + libgfortran 15.2.0 h69a702a_18 conda-forge 28kB
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#10 15.41 + ocl-icd 2.3.3 hb9d3cd8_0 conda-forge 107kB
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#10 15.41 + python 3.12.10 h9e4cc4f_0_cpython conda-forge 31MB
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#10 15.41 + libgfortran-ng 15.2.0 h69a702a_18 conda-forge 28kB
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#10 15.41 + libopenblas 0.3.32 pthreads_h94d23a6_0 conda-forge 6MB
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#10 15.41 + ocl-icd-system 1.0.0 1 conda-forge 4kB
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#10 15.41 + openmpi 4.1.6 hc5af2df_101 conda-forge 4MB
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#10 15.41 + libblas 3.11.0 6_h4a7cf45_openblas conda-forge 19kB
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#10 15.41 + packaging 26.2 pyhc364b38_0 conda-forge 92kB
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#10 15.41 + setuptools 82.0.1 pyh332efcf_0 conda-forge 640kB
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#10 15.41 + wheel 0.47.0 pyhd8ed1ab_0 conda-forge 33kB
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#10 15.41 + pip 26.1.1 pyh8b19718_0 conda-forge 1MB
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#10 15.41 + legacy-cgi 2.6.4 pyhcf101f3_0 conda-forge 20kB
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#10 15.41 + hmmer 3.4 hb6cb901_4 bioconda 12MB
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#10 15.41 + numpy 2.4.3 py312h33ff503_0 conda-forge 9MB
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#10 15.41 + biopython 1.85 py312h4c3975b_2 conda-forge 3MB
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#10 15.41 + scipy 1.17.1 py312h54fa4ab_0 conda-forge 17MB
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#10 15.41 + openmm 8.3.1 py312h50c43f0_0 conda-forge 13MB
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#10 15.41 + anarci 2024.05.21 pyhdfd78af_0 bioconda 1MB
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#10 15.41 + pdbfixer 1.12 pyhd8ed1ab_1 conda-forge 546kB
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#10 15.41
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#10 15.41 Summary:
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#10 15.41 Install: 54 packages
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#10 15.41 Total download: 353MB
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#10 15.41 ───────────────────────────────────────────────────────────────────────────────
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#10 15.41 Transaction starting
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#10 21.24
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#10 21.39
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#10 21.39 For Linux 64, Open MPI is built with CUDA awareness but this support is disabled by default.
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#10 21.39 To enable it, please set the environment variable OMPI_MCA_opal_cuda_support=true before
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#10 21.39 launching your MPI processes. Equivalently, you can set the MCA parameter in the command line:
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#10 21.39 mpiexec --mca opal_cuda_support 1 ...
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#10 21.39 In addition, the UCX support is also built but disabled by default.
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#10 21.39 To enable it, first install UCX (conda install -c conda-forge ucx). Then, set the environment
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#10 21.39 variables OMPI_MCA_pml="ucx" OMPI_MCA_osc="ucx" before launching your MPI processes.
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#10 21.39 Equivalently, you can set the MCA parameters in the command line:
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#10 21.39 mpiexec --mca pml ucx --mca osc ucx ...
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#10 21.39 Note that you might also need to set UCX_MEMTYPE_CACHE=n for CUDA awareness via UCX.
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#10 21.39 Please consult UCX's documentation for detail.
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#10 21.39
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#10 22.51
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#10 22.51 Transaction finished
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#10 22.51
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#10 22.51 To activate this environment, use:
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#10 22.51
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#10 22.51 micromamba activate base
|
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#10 22.51
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#10 22.51 Or to execute a single command in this environment, use:
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#10 22.51
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#10 22.51 micromamba run -n base mycommand
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#10 22.51
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#10 22.54 Collect information..
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#10 22.54 Cleaning index cache..
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#10 22.70 Cleaning lock files..
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#10 22.70 Package file Size
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#10 22.70 ───────────────────────────────────────────────────────────────
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#10 22.70 /opt/conda/pkgs
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#10 22.70 ───────────────────────────────────────────────────────────────
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#10 22.70
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#10 22.70 _openmp_mutex-4.5-20_gnu.conda 29kB
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#10 22.70 anarci-2024.05.21-pyhdfd78af_0.tar.bz2 1MB
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#10 22.70 biopython-1.85-py312h4c3975b_2.conda 3MB
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#10 22.70 bzip2-1.0.8-hda65f42_9.conda 260kB
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#10 22.70 ca-certificates-2026.4.22-hbd8a1cb_0.conda 131kB
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#10 22.70 cuda-nvrtc-12.9.86-hecca717_1.conda 67MB
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#10 22.70 cuda-version-12.9-h4f385c5_3.conda 22kB
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#10 22.70 gsl-2.7-he838d99_0.tar.bz2 3MB
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#10 22.70 hmmer-3.4-hb6cb901_4.tar.bz2 12MB
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#10 22.70 ld_impl_linux-64-2.45.1-default_hbd61a6d_102.conda 728kB
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#10 22.70 legacy-cgi-2.6.4-pyhcf101f3_0.conda 20kB
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#10 22.70 libblas-3.11.0-6_h4a7cf45_openblas.conda 19kB
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215
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#10 22.70 libcblas-3.11.0-6_h0358290_openblas.conda 19kB
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#10 22.70 libcufft-11.4.1.4-hecca717_1.conda 162MB
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217
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#10 22.70 libexpat-2.8.0-hecca717_0.conda 77kB
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#10 22.70 libffi-3.4.6-h2dba641_1.conda 57kB
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#10 22.70 libgcc-15.2.0-he0feb66_18.conda 1MB
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#10 22.70 libgcc-ng-15.2.0-h69a702a_18.conda 28kB
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#10 22.70 libgfortran-15.2.0-h69a702a_18.conda 28kB
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#10 22.70 libgfortran-ng-15.2.0-h69a702a_18.conda 28kB
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#10 22.70 libgfortran5-15.2.0-h68bc16d_18.conda 2MB
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#10 22.70 libgomp-15.2.0-he0feb66_18.conda 603kB
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#10 22.70 liblapack-3.11.0-6_h47877c9_openblas.conda 19kB
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#10 22.70 liblzma-5.8.3-hb03c661_0.conda 113kB
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#10 22.70 libnsl-2.0.1-hb9d3cd8_1.conda 34kB
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#10 22.70 libopenblas-0.3.32-pthreads_h94d23a6_0.conda 6MB
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#10 22.70 libsqlite-3.53.1-h0c1763c_0.conda 955kB
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#10 22.70 libstdcxx-15.2.0-h934c35e_18.conda 6MB
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#10 22.70 libstdcxx-ng-15.2.0-hdf11a46_18.conda 28kB
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#10 22.70 libuuid-2.42-h5347b49_0.conda 40kB
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#10 22.70 libxcrypt-4.4.36-hd590300_1.conda 100kB
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#10 22.70 libzlib-1.3.2-h25fd6f3_2.conda 64kB
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#10 22.70 mpi-1.0-openmpi.tar.bz2 4kB
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#10 22.70 ncurses-6.6-hdb14827_0.conda 919kB
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#10 22.70 numpy-2.4.3-py312h33ff503_0.conda 9MB
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#10 22.70 ocl-icd-2.3.3-hb9d3cd8_0.conda 107kB
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#10 22.70 ocl-icd-system-1.0.0-1.tar.bz2 4kB
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#10 22.70 opencl-headers-2025.06.13-hecca717_0.conda 56kB
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241
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#10 22.70 openmm-8.3.1-py312h50c43f0_0.conda 13MB
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242
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platforma-open.milaboratories.3d-structure-prediction.software.py-docker.e8cc067379a9: digest: sha256:f69985f8638c8bbd1e9a6aee8d3e2b1f9854bcb273dc06a63daf3882fb3252c6 size: 3860
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package/CHANGELOG.md
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package/Dockerfile
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@@ -33,6 +33,8 @@ RUN micromamba install -y -n base -c bioconda -c conda-forge \
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biopython=1.85 \
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openmm=8.3.1 \
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pdbfixer=1.12.0 \
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numpy=2.4.3 \
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scipy=1.17.1 \
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&& micromamba clean --all --yes
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# Activate the base env for every subsequent RUN/CMD layer so pip and
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ARG MAMBA_DOCKERFILE_ACTIVATE=1
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ENV PATH=/opt/conda/bin:$PATH
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# Make conda's libstdc++ (and friends) win over the older system libs in
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# /lib/x86_64-linux-gnu. Pip-installed extension wheels (manylinux2014+)
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# expect a recent CXXABI; the base image's system libstdc++ predates it.
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ENV LD_LIBRARY_PATH=/opt/conda/lib
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# Layer pip-only deps (ImmuneBuilder + CPU torch). Anything bioconda
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# already provides is re-resolved by pip; pinned versions in
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# requirements.txt match the conda packages so this is a no-op for those.
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@@ -1 +1 @@
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{"type":"python","platform":"linux-x64","registryURL":"https://bin.pl-open.science/","registryName":"platforma-open","remoteArtifactLocation":"software/platforma-open/milaboratories.3d-structure-prediction.software/py-archive/1.0.
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{"type":"python","platform":"linux-x64","registryURL":"https://bin.pl-open.science/","registryName":"platforma-open","remoteArtifactLocation":"software/platforma-open/milaboratories.3d-structure-prediction.software/py-archive/1.0.3.tgz","uploadPath":"software/platforma-open/milaboratories.3d-structure-prediction.software/py-archive/1.0.3.tgz"}
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{"type":"docker","platform":"linux-x64","remoteArtifactLocation":"containers.pl-open.science/milaboratories/pl-containers:platforma-open.milaboratories.3d-structure-prediction.software.py-docker.
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{"type":"docker","platform":"linux-x64","remoteArtifactLocation":"containers.pl-open.science/milaboratories/pl-containers:platforma-open.milaboratories.3d-structure-prediction.software.py-docker.e8cc067379a9","entrypoint":["/usr/local/bin/_entrypoint.sh"]}
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-
{"name":"@platforma-open/milaboratories.3d-structure-prediction.software:immunebuilder-predict","docker":{"tag":"containers.pl-open.science/milaboratories/pl-containers:platforma-open.milaboratories.3d-structure-prediction.software.py-docker.
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{"name":"@platforma-open/milaboratories.3d-structure-prediction.software:immunebuilder-predict","docker":{"tag":"containers.pl-open.science/milaboratories/pl-containers:platforma-open.milaboratories.3d-structure-prediction.software.py-docker.e8cc067379a9","entrypoint":["/usr/local/bin/_entrypoint.sh"],"cmd":["python","/app/run_immunebuilder.py"],"pkg":"/app"},"binary":{"type":"python","registry":"platforma-open","package":"software/platforma-open/milaboratories.3d-structure-prediction.software/py-archive/1.0.3.tgz","cmd":["python","{pkg}/run_immunebuilder.py"],"envVars":[],"runEnv":{"name":"@platforma-open/milaboratories.runenv-python-3:3.12.10-atls","type":"python","registry":"platforma-open","package":"software/platforma-open/milaboratories.runenv-python-3.12.10-atls/main/1.2.7-{os}-{arch}.tgz","python-version":"3.12.10","envVars":[],"binDir":"bin"},"toolset":"pip","dependencies":{"requirements":"requirements.txt"}}}
|
package/package.json
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