starting from ubuntu 24 with r-base installed
+ +sudo apt install -y cmake libssl-dev libudunits2-dev libgdal-dev
+
+ gdal-bin
+
+ Rscript -e "install.packages("spOccupancy")Rscript -e "install.packages("stars")Rscript -e "install.packages("ggplot2")Rscript 5...5.Analysis_spOccupancy_MultiSp_SpatInteg_Summer.RSingularity is used to package the application for a SLURM supercomputer.
+ +#
+ Build `run.sif` from `Singularity.def` on local machine with sudo:
+
+ sudo singularity build run.sif Singularity.def
+
+
+ # transfer .sif to supercomputer
+
+ rsync -hazv run.sif tylarmurray@circe.rc.usf.edu:.
+
+
+ mkdir run##, cd into it, then:
TEMPLATE=run03
+
+ mkdir old-slurm
+
+ cat "new run from template $TEMPLATE" >
+ README.md
+
+
+ ln -s ../data/Shapes Shapes
+
+ ln -s ../data/spOccupancy_MultiSpp_FullArea spOccupancy_MultiSpp_FullArea
+
+ ln -s ../data/Grid_OccEnv_Seasonal.txt Grid_OccEnv_Seasonal.txt
+
+
+ cp ../$TEMPLATE/5.Analysis_spOccupancy_MultiSp_SpatInteg_Summer.R
+ .
+
+ cp ../$TEMPLATE/submit.sh .
+
+
+ git add README.md 5.Analysis_spOccupancy_MultiSp_SpatInteg_Summer.R submit.sh
+
+ git add -f Grid_OccEnv_Seasonal.txt Shapes spOccupancy_MultiSpp_FullAreaNOTE: for *winter runs, the file is still named *_Summer.R, just
+ use a different TEMPLATE.
--force A flag indicating that the output\
\ file should be overwritten if it already exists. Default = Do NOT override existing\
\ output file
This\ \ project follows the all-contributors specification. Contributions of any kind welcome!
\n" - stargazers_count: 1957 + stargazers_count: 1959 subscribers_count: 37 topics: - computer-vision @@ -72560,7 +72674,7 @@ UniversalDataTool/universal-data-tool: - labeling - labeling-tool - hacktoberfest - updated_at: 1731590757.0 + updated_at: 1732477744.0 VALENCE-software/VALENCE: data_format: 2 description: quantum chemistry software @@ -90661,8 +90775,8 @@ bids-apps/ndmg: data_format: 2 description: BIDS app for NeuroData's MRI to Graphs pipeline filenames: - - Singularity.v0.1.0 - Singularity + - Singularity.v0.1.0 full_name: bids-apps/ndmg latest_release: null readme: "![\"Status\"](\"https://github.com/pscedu/singularity-rich-cli/actions/workflows/pretty.yml/badge.svg\"\){kind=icon}
\n![\"Issue\"](\"https://img.shields.io/github/issues/pscedu/singularity-rich-cli\"\)
![\"forks\"](\"https://img.shields.io/github/forks/pscedu/singularity-rich-cli\"\)
![\"Stars\"](\"https://img.shields.io/github/stars/pscedu/singularity-rich-cli\"\)
Takes .cel files and creates qc plots as well as normalising the data
\n\![\"Build](\"https://travis-ci.org/qbicsoftware/microarray-qc-workflow.svg?branch=master\"\)
![\"install](\"https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg\"\){kind=icon}
![\"Docker\"](\"https://img.shields.io/docker/automated/microarray-qc-workflow.svg\"\)
An Nvidia GPU with CUDA support for GPU acceleration.
\n\ -Basic Unix/Linux knowledge.
\nAn Nvidia GPU with CUDA support for GPU acceleration.
\nBasic Unix/Linux knowledge.
\nTested with python 3.6 and 2.7
\nEasy installation of dependencies\ - \ with conda
\n![\"License\"](\"https://img.shields.io/github/license/pscedu/singularity-rich-cli\"\)
![\"Nextflow\"](\"https://img.shields.io/badge/nextflow-%E2%89%A50.30.0-brightgreen.svg\"\){kind=icon}
![\"Singularity](\"https://img.shields.io/badge/singularity-available-7E4C74.svg\"\){kind=icon}
![\"Python](\"https://github.com/tbepler/topaz/actions/workflows/ci.yml/badge.svg\"\){kind=icon}
conda install numpy pandas scikit-learn\nconda install\
- \ -c pytorch pytorch torchvision\nFor more info on installing\ - \ pytorch for your CUDA version see https://pytorch.org/get-started/locally/
\ngit\
- \ clone https://github.com/tbepler/topaz\nMove to the source code directory
\ncd topaz\nBy default, this will be the most recent version of the topaz source code.\ - \ To install a specific older version, checkout that commit. For example, for\ - \ v0.1.0 of Topaz:
\ngit checkout v0.1.0\nNote\ - \ that older Topaz versions may have different dependencies. Refer to the README\ - \ for the specific Topaz version.
\nInstall Topaz into your Python path\ - \ including the topaz command line interface
\npip install .\nTo install for development use
\npip install -e .\nTopaz is also available through SBGrid.
\n\nThe tutorials are presented\ - \ in Jupyter notebooks. Please install Jupyter following the instructions here.
\n\nThe tutorial\ - \ data can be downloaded here.
\nTo run the tutorial steps on your own system,\
- \ you will need to install \n Easy installation of dependencies with conda For more info on installing pytorch for your\
+ \ CUDA version see https://pytorch.org/get-started/locally/ Move to the source code directory By default, this will be the most recent\
+ \ version of the topaz source code. To install a specific older version, checkout\
+ \ that commit. For example, for v0.1.0 of Topaz: Note that older Topaz versions may have different\
+ \ dependencies. Refer to the README for the specific Topaz version. Install\
+ \ Topaz into your Python path including the topaz command line interface To install for development use Topaz is also available through\
+ \ SBGrid. The tutorials are presented in Jupyter notebooks. Please\
+ \ install Jupyter following the instructions here. The tutorial data can be downloaded here. To run the tutorial steps on your own system, you\
+ \ will need to install Jupyter and matplotlib\
\ which is used for visualization. With Anaconda this can be done with: If you installed\
@@ -220042,7 +220182,7 @@ tbepler/topaz:
For general help, questions, suggestions, tips, and installation/setup assistance,\
\ please take a look at our new Discussion section.
\nconda\
+ \ install numpy pandas scikit-learn h5py tqdm\nconda install -c pytorch pytorch\
+ \ torchvision\n
\n\
+ git clone https://github.com/tbepler/topaz\n\nInstall Topaz
\ncd topaz\n
\ngit checkout\
+ \ v0.1.0\n
\npip install .\n
\n\npip install -e .\n\nTutorial
\nconda install jupyter matplotlib\n
There is hs-hdf5.\
\ It covers more\nfunctionality of HDF5 than this package, but the API is lower-level.