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- ** Admin** : [ Getting started] ( admin/getting_started.md ) * [ Setting up an analysis] ( admin/setting_up_an_analysis_guidelines.md ) * [ Data Management] ( admin/data_management.md ) * [ Reproducible Research] ( admin/reproducible_research.md ) * [ Methods for manuscripts] ( admin/method_snippets.md ) * [ Downloading data] ( admin/download_data.md ) * [ Globus] ( admin/Globus.md ) * [ Acknowledging funding] ( admin/acknowledging_funding ) * [ Initial consults] ( admin/initial_consults.md ) * [ Chargeback models] ( admin/chargeback_models.md ) * [ Archiving project folders] ( admin/archive_folders_to_standby.md ) * [ Consulting resources] ( admin/consulting_resources.md ) * [ Pull for knowledge work instead of push] ( https://dspace.mit.edu/bitstream/handle/1721.1/115364/Repenning_Pull%20for%20Knowledge%20Work_Full.pdf?sequence=1&isAllowed=y ) * [ Scripts for tracking storage on O2] ( admin/scripts_for_data_management_on_o2 )
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+ ** Admin** : [ Getting started] ( admin/getting_started.md ) * [ Setting up an analysis] ( admin/setting_up_an_analysis_guidelines.md ) * [ Data Management] ( admin/data_management.md ) * [ Reproducible Research] ( admin/reproducible_research.md ) * [ Methods for manuscripts] ( admin/method_snippets.md ) * [ Downloading data] ( admin/download_data.md ) * [ Globus] ( admin/Globus.md ) * [ Acknowledging funding] ( admin/acknowledging_funding ) * [ Initial consults] ( admin/initial_consults.md ) * [ Chargeback models] ( admin/chargeback_models.md ) * [ Archiving project folders] ( admin/archive_folders_to_standby.md ) * [ Consulting resources] ( admin/consulting_resources.md ) * [ Pull for knowledge work instead of push] ( https://dspace.mit.edu/bitstream/handle/1721.1/115364/Repenning_Pull%20for%20Knowledge%20Work_Full.pdf?sequence=1&isAllowed=y ) * [ Scripts for tracking storage on O2] ( admin/scripts_for_data_management_on_o2 )
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- ** RC** : * [ O2 OpenPortal] ( rc/O2_portal_errors.md ) * [ Connection to HPC] ( rc/connection-to-hpc.md ) * [ Keep command alive] ( rc/keepalive.md ) * [ IPython notebook] ( rc/ipython-notebook-on-O2.md ) * [ Manage files] ( rc/manage-files.md ) * [ O2 tips] ( rc/O2-tips.md ) * [ Scheduler] ( rc/scheduler.md ) * [ Jupyter notebooks] ( rc/jupyter_notebooks.md ) * [ tmux tips] ( rc/tmux.md ) * [ FAS virtual desktops] ( rc/openondemand.md ) * [ Arrays in Slurm] ( rc/arrays_in_slurm.md ) * [ Common O2 portal Issues] ( rc/O2_portal_errors.md )
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+ ** RC** : * [ O2 OpenPortal] ( rc/O2_portal_errors.md ) * [ Connection to HPC] ( rc/connection-to-hpc.md ) * [ FASRC ] ( admin/FASRC.md ) * [ Keep command alive] ( rc/keepalive.md ) * [ IPython notebook] ( rc/ipython-notebook-on-O2.md ) * [ Manage files] ( rc/manage-files.md ) * [ O2 tips] ( rc/O2-tips.md ) * [ Scheduler] ( rc/scheduler.md ) * [ Jupyter notebooks] ( rc/jupyter_notebooks.md ) * [ tmux tips] ( rc/tmux.md ) * [ FAS virtual desktops] ( rc/openondemand.md ) * [ Arrays in Slurm] ( rc/arrays_in_slurm.md ) * [ Common O2 portal Issues] ( rc/O2_portal_errors.md )
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** bcbio** : [ docs] ( https://bcbio-nextgen.readthedocs.io/en/latest/ ) * [ issues] ( https://github.com/bcbio/bcbio-nextgen/issues ) * [ validation] ( https://github.com/bcbio/bcbio_validations ) * [ running in parallel] ( https://bcbio-nextgen.readthedocs.io/en/latest/contents/parallel.html ) * [ genomes] ( bcbio/bcbio_genomes.md ) * [ tips] ( bcbio/bcbio_tips.md ) * [ RNA-seq workflow by Mary] ( bcbio/bcbio_workflow_mary.md ) * [ installation by Michael] ( https://steinbaugh.com/posts/install-bcbio.html ) * [ installation by Sergey] ( https://github.com/naumenko-sa/bioscripts/blob/master/bcbio/bcbio.upgrade.sh ) * [ RNA-seq workflow by Systems Pharmacology lab] ( https://labsyspharm.github.io/rnaseq/ ) * [ gtf/gff validators] ( bcbio/gtf_gff_validator.md ) * [ Create hybrid mammal virus genome] ( bcbio/Creating_Hybrid_Mammal_Viral_Reference_Genome.md ) * [ python package in 2022] ( https://mathspp.com/blog/how-to-create-a-python-package-in-2022 )
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