Files in richelbilderbeek/peregrine
Work With The Groninger Peregrine Computer Cluster

.Rbuildignore

.covrignore

.github/.gitignore

.github/workflows/R-CMD-check.yaml

.github/workflows/check_bash_style.yaml

.gitignore

DESCRIPTION

NAMESPACE

NEWS.md R/are_pff_experiments.R R/check_pff_alignment_params.R R/check_pff_beast2_options.R R/check_pff_experiment.R R/check_pff_experiments.R R/check_pff_inference_model.R R/check_pff_mcmc.R R/check_pff_pir_params.R R/check_pff_twinning_params.R R/count_jobs.R R/count_regular_jobs.R R/count_vulture_jobs.R R/create_all_pff_experiments.R R/create_pff_beast2_options.R R/create_pff_mcmc.R R/create_pff_pir_params.R R/create_test_pff_gen_experiment.R

R/create_test_pff_pir_params.R

R/default_params_doc.R R/get_pff_tempdir.R R/get_pff_tempfile.R R/is_on_peregrine.R R/is_on_peregrine_login_node.R R/is_on_peregrine_worker_node.R R/is_pff.R R/is_pff_beast2_options.R R/is_pff_experiment.R R/time_str_to_n_sec.R R/time_strs_to_n_secs.R R/to_pff.R R/to_pff_alignment_params.R R/to_pff_beast2_options.R R/to_pff_experiment.R R/to_pff_experiments.R R/to_pff_mcmc.R R/to_pff_pir_params.R R/to_pff_twinning_params.R README.md doc/README.md

doc/bash_arrays/create_bash_arrays.sh

doc/bash_arrays/show_bash_arrays.sh

doc/beast2_on_peregrine/LICENSE

doc/beast2_on_peregrine/README.md

doc/beast2_on_peregrine/clean.sh

doc/beast2_on_peregrine/example.xml

doc/beast2_on_peregrine/sbatch_me.sh

doc/data_race/add_a.sh

doc/data_race/add_b.sh

doc/data_race/multirun.sh

doc/data_race/run.sh

doc/data_race/shakespeare.html

doc/dependencies.dot

doc/dependencies.png

doc/dependencies.ps

doc/independent_jobs.odp

doc/independent_jobs.pdf doc/install_rstan/README.md doc/install_rstan/install_rstan.R

doc/install_rstan/install_rstan.sh

doc/intro_to_peregrine/create_input_files_general

doc/intro_to_peregrine/install_raket

doc/job_dependencies.odp

doc/job_dependencies.pdf doc/job_with_replicates/README.md

doc/job_with_replicates/job_with_rep

doc/job_with_replicates/run

doc/job_without_replicate/README.md

doc/job_without_replicate/job_without_rep

doc/job_without_replicate/run

doc/jobs_in_parallel/README.md

doc/jobs_in_parallel/job1_master.sh

doc/jobs_in_parallel/job1_slave.sh

doc/jobs_in_parallel/job2.sh

doc/jobs_in_parallel/run.sh

doc/jobs_in_parallel_fail/README.md

doc/jobs_in_parallel_fail/job_1.sh

doc/jobs_in_parallel_fail/job_2_master.sh

doc/jobs_in_parallel_fail/job_2_slave.sh

doc/jobs_in_parallel_fail/job_3.sh

doc/jobs_in_parallel_fail/jobs.sh

doc/jobs_in_sequence/README.md

doc/jobs_in_sequence/job1.sh

doc/jobs_in_sequence/job2.sh

doc/jobs_in_sequence/run.sh

doc/jobs_in_sequence_and_parallel/README.md

doc/jobs_in_sequence_and_parallel/job1.sh

doc/jobs_in_sequence_and_parallel/job2_master.sh

doc/jobs_in_sequence_and_parallel/job2_slave.sh

doc/jobs_in_sequence_and_parallel/job3.sh

doc/jobs_in_sequence_and_parallel/run.sh

doc/jobs_in_sequence_by_hand/README.md

doc/jobs_in_sequence_by_hand/job1.sh

doc/jobs_in_sequence_by_hand/job2.sh

doc/jobs_in_sequence_with_parameter/README.md

doc/jobs_in_sequence_with_parameter/job1.sh

doc/jobs_in_sequence_with_parameter/job2.sh

doc/jobs_in_sequence_with_parameter/out.txt

doc/jobs_in_sequence_with_parameter/run.sh

doc/jobs_in_tandem_with_echo/README.md

doc/jobs_in_tandem_with_echo/jobs.sh

doc/jobs_in_tandem_with_scripts/README.md

doc/jobs_in_tandem_with_scripts/job_1.sh

doc/jobs_in_tandem_with_scripts/job_2.sh

doc/jobs_in_tandem_with_scripts/job_3.sh

doc/jobs_in_tandem_with_scripts/jobs.sh

doc/simple_job/README.md

doc/simple_job/run.sh

doc/simple_job/simple_job.sh

doc/while_file_absent/while_file_absent.sh

inst/extdata/squeue.txt

man/are_pff_experiments.Rd man/check_pff_alignment_params.Rd man/check_pff_beast2_options.Rd man/check_pff_experiment.Rd man/check_pff_experiments.Rd man/check_pff_inference_model.Rd man/check_pff_mcmc.Rd man/check_pff_pir_params.Rd man/check_pff_twinning_params.Rd man/count_jobs.Rd man/count_regular_jobs.Rd man/count_vulture_jobs.Rd man/create_all_pff_experiments.Rd man/create_pff_beast2_options.Rd man/create_pff_mcmc.Rd man/create_pff_pir_params.Rd man/create_test_pff_gen_experiment.Rd man/default_params_doc.Rd

man/figures/AppVeyor.png

man/figures/Codecov.png

man/figures/GitHubActions.png

man/get_pff_tempdir.Rd man/get_pff_tempfile.Rd man/is_on_peregrine.Rd man/is_on_peregrine_login_node.Rd man/is_on_peregrine_worker_node.Rd man/is_pff.Rd man/is_pff_beast2_options.Rd man/is_pff_experiment.Rd man/time_str_to_n_sec.Rd man/time_strs_to_n_secs.Rd man/to_pff.Rd man/to_pff_alignment_params.Rd man/to_pff_beast2_options.Rd man/to_pff_experiment.Rd man/to_pff_experiments.Rd man/to_pff_mcmc.Rd man/to_pff_pir_params.Rd man/to_pff_twinning_params.Rd

peregrine.Rproj

pics/CC-BY-NC-SA.png

pics/Codecov.png

pics/GitHubActions.png

pics/README.md

pics/peregrine_falcon.jpg

scripts/.gitignore

scripts/Makefile

scripts/README.md

scripts/alignment.png

scripts/check_beast2.sh

scripts/check_mcbette.sh

scripts/check_mhcnuggetsr.sh

scripts/collect_running_job_ids.sh

scripts/collect_running_regular_job_ids.sh

scripts/collect_running_vulture_job_ids.sh

scripts/count_jobs.sh

scripts/count_regular_jobs.sh

scripts/count_vulture_jobs.sh

scripts/email_me.sh

scripts/ggplot.png

scripts/hello_world.R

scripts/install_babette.sh

scripts/install_bbbq.sh

scripts/install_beast2.sh

scripts/install_bianchietal2017.sh

scripts/install_cobalt.sh

scripts/install_cobaltr.sh

scripts/install_csv2latex.sh

scripts/install_epiprepreds.sh

scripts/install_epitope_prediction.sh

scripts/install_hdf5r.sh

scripts/install_magick.sh

scripts/install_mcbette.sh

scripts/install_mhcnpreds.sh

scripts/install_mhcnuggets.sh

scripts/install_mhcnuggetsr.sh

scripts/install_msa.sh

scripts/install_ncbi.sh

scripts/install_ncbi_peregrine.sh

scripts/install_netmhc2pan.sh

scripts/install_nmhc2ppreds.sh

scripts/install_peregrine.sh

scripts/install_pip.sh

scripts/install_pirouette.sh

scripts/install_plinkr.sh

scripts/install_plinks.sh

scripts/install_prosefi.sh

scripts/install_pureseqtm.sh

scripts/install_pureseqtmr.sh

scripts/install_razzo.sh

scripts/install_sprentrez.sh

scripts/install_tmhmm.sh

scripts/is_on_peregrine.sh

scripts/make.sh

scripts/run_make.sh

scripts/run_pir.R

scripts/run_r_cmd.sh

scripts/run_r_script.sh

scripts/run_r_script_with_x.sh

scripts/test_is_pff.R scripts/test_plot_alignment.R scripts/test_plot_ggplot.R

scripts/uninstall_beast2.sh

scripts/uninstall_mhcnuggets.sh

scripts/update_packages.sh

tests/testthat.R tests/testthat/test-are_pff_experiments.R tests/testthat/test-count_jobs.R tests/testthat/test-count_regular_jobs.R tests/testthat/test-count_vulture_jobs.R tests/testthat/test-create_all_pff_experiments.R tests/testthat/test-create_pff_alignment_params.R tests/testthat/test-create_pff_pir_params.R tests/testthat/test-create_pff_twinning_params.R tests/testthat/test-create_test_pff_gen_experiment.R

tests/testthat/test-create_test_pff_pir_params.R

tests/testthat/test-get_pff_tempdir.R

tests/testthat/test-get_pff_tempfile.R

richelbilderbeek/peregrine documentation built on Jan. 3, 2024, 7:42 p.m.

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richelbilderbeek/peregrine
Work With The Groninger Peregrine Computer Cluster

Files in richelbilderbeek/peregrine
Work With The Groninger Peregrine Computer Cluster

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richelbilderbeek/peregrine Work With The Groninger Peregrine Computer Cluster

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richelbilderbeek/peregrine
Work With The Groninger Peregrine Computer Cluster

Files in richelbilderbeek/peregrine
Work With The Groninger Peregrine Computer Cluster