From 387257e8fbb391986cf3fcaeb5ea0610dd42d8bd Mon Sep 17 00:00:00 2001 From: Jan Mandel Date: Mon, 11 Mar 2024 10:57:41 -0600 Subject: [PATCH] singularity from alderaan --- docs/singularity.md | 55 ++++++++++++++++++++++++++++++++++++++++------------- 1 file changed, 42 insertions(+), 13 deletions(-) diff --git a/docs/singularity.md b/docs/singularity.md index 84f73ed..d7ef897 100644 --- a/docs/singularity.md +++ b/docs/singularity.md @@ -97,53 +97,82 @@ You can see that the script is exactly like installing your own Linux machine af Then start a shell in the container as above, and you can do whatever you normally do to examine softwares and their versions. -Note: building a container will pick up current version of software, so the versions below will change when containers are rebuilt. +Note: Rebuilding a container usually picks up current version of software, so the versions listed below may change when containers are rebuilt. ### bfctools.sif -Bioinformatics sofware bfctools 1.15.1 for processing and analyzing sequencing data. +Bioinformatics sofware bfctools 1.15.1 for processing and analyzing sequencing data. Based on Ubuntu 20.04 with Development Tools. + +### bio-lowry.sif + +Ubuntu 20.04 with Development Tools and biology packages bbmap megahit megabat checkm gtdbtkUbuntu 20.04 with Development Tools and biology packages bbmap megahit megabat checkm gtdbtk. + +### biopython.sif + +Biopython 1.78 in Anacoda 3 Python 3.9.13 based on Ubuntu 20.04. + +### cactus-gpu.sif + +Imported Docker quay.io/comparative-genomics-toolkit/cactus:v2.5.2-gpu ### CentOS8-DevelopmentTools.sif CentOS Linux 8.4.2105, gcc 8.4.1 and standard Development Tools from Centos. +### cuda-116.sif + +Imported Docker nvidia/cuda:11.6.1-devel-ubuntu20.04 + +### cuda-120.sif + +Ubuntu 22.04 with cuda 12.0, NVIDIA compilers, tensorflow, pytorch, and other common machine learning packages + ### go.sif -The Go language with gcc/gfortran 9 and development tools, based on Ubuntu. +The Go language with gcc/gfortran 9 and development tools, based on Ubuntu 20.04 ### mixtures.sif -R 4.1.2 with numerous standard and custom packages and datasets, see the definition file. +Custom container for the mixtures project. R 4.1.2 with raresim, plink2, Python with regenie, bcftools, pliknk,hapgen2, bedtools. etc., and datasets. Based on Ubuntu 22.04 + +### poppler.sif + +Container with python3-poppler-qt5, tensorflow, sklearn, matplotlib, keras, keras-tuner, tensorflow_datasets, pdf2image, jupyterhub, jupyter and pandas. No CUDA. Based on Ubuntu 22.04 ### pyscipopt-geopandas.sif -Optimization software [PySCIPOpt](https://pypi.org/project/PySCIPOpt) pyscipopt 4.2.0, ipopt, glpk, pyomo, gurobi, with geopandas. +Optimization software [PySCIPOpt](https://pypi.org/project/PySCIPOpt) pyscipopt 4.2.0, ipopt, glpk, pyomo, gurobi, with geopandas in miniconda and Ubuntu 21.04 ### qvina.sif -Modecular chemistry software [QuickVina](https://github.com/QVina/qvina), gcc, gfortran, python3. +Modecular chemistry software [QuickVina](https://github.com/QVina/qvina), gcc, gfortran, python3 on Ubuntu 21.04 ### sagemath.sif -[SageMath](https://www.sagemath.org) mathematical sofrware, with python 3.9.5, R 4.0.4, and others. +[SageMath](https://www.sagemath.org) mathematical sofrware, SAGE 9.5 with R 4.2.1 and Python 3.10.6 on Ubuntu 22.04. ### saige.sif Genomic software [saige](https://saigegit.github.io/SAIGE-doc/docs/Installation.html) container from docker image wzhou88/saige:1.1.6, comes with R 3.6.3. -### tensorflow.sif +### tensorflow-1.4-new.sif -python3.8.20 (gcc 9.3.9) as python 3, with numpy 1.22.2 and tensorflow 2.8.0 with sklearn matplotlib keras keras-tuner tensorflow_datasets pandas opencv-python-headless, -CUDA 11.4, jupyter 1.0.0, jupyterhub 2.1.1 +Cuda 11, tensorflow 1.4, sklearn, matplotlib, keras, keras-tuner, tensorflow_datasets, pdf2image and pandas, on Ubuntu 20.04 -Note: tensorflow will run with or without GPU, but it will crash python on most colibri nodes because their CPUs and GPUs are too old. +Note: Tensorflow will run with or without GPU, but it will crash python on most colibri nodes because their CPUs and GPUs are too old. -### tensorflow-v1.2.sif and tensorflow-v1.3.sif +### tensorflow-v1.4.sif -An earlier versions of tensorflow, which can run on older CPUs. +cuda 11, tensorflow 1.4, sklearn, matplotlib, keras, keras-tuner, tensorflow_datasets, pdf2image and pandas. +### tensorflow-2.6.0-cuda-1.1.2.sif +NVIDIA nvidia/cuda:11.2.2-base-ubuntu20.04 with Anaconda and cuDNN 8 added. +### tensorflow.sif +Cuda 11, tensorflow, sklearn, matplotlib, keras, keras-tuner, tensorflow_datasets, pdf2image, jupyterhub, jupyter and pandas. +### tensorflow_latest-gpu-jupyter.sif +Cuda 11, tensorflow 1.4, sklearn, matplotlib, keras, keras-tuner, tensorflow_datasets, pdf2image and pandas. \ No newline at end of file -- 2.11.4.GIT