====== How to ======

This wiki is really my digital notebook of things I found useful and weren't one google/stackoverflow/chatgpt search away.

You can reach me on [[https://twitter.com/dr_jpe|twitter]] or via email at my idea of a spam-proof address here:
<code bash>echo "jp.is.king" | perl -ne "s/\./@/g; print" | perl -ne "s/is\@king/bitsilla/g; print" | perl -ne "s/$/.com/; print"</code>

Below find some common tasks I keep returning to or are of general interest (or scarce on the www).

===== Anaconda (Python) =====

  * How do I [[howto:create_python_environment_for_study_unit_xxx|create a python environment for study unit XXX1234]]?
  * How do I [[howto:export_an_anaconda_environment_to_a_file|export an Anaconda environment to a file (for distribution)]]?

===== Cassandra =====

  * How do I [[howto:cassandra_install|install cassandra]]?
  * How do I [[howto:cassandra_fix_upgrade_ubuntu|fix Cassandra after an Ubuntu upgrade]]?

===== Bash & Linux (Ubuntu, mostly) =====

  * How do I [[howto:linux_motd|change the MOTD banner]]?
  * How do I [[howto:linux_gnu_parallel|run tasks in parallel using GNU parallel (e.g. compress files of a certain kind)]]?
  * How do I [[howto:linux_split_file_first_col|split a file based on the first column (e.g. of a csv file)]]?
  * How do I [[howto:linux_insert_header_in_all_files|insert the same header in all files]]?

===== Git =====

  * How do I [[howto:git_create_tag_from_branch|create a tag from a branch (and remove the branch)]] ?

===== JupyterHub =====

  * How do I [[howto:jupyterhub_run|run JupyterHub on Titan]] ?

===== Molgenis (Life sciences software) =====

  * How do I [[howto:molgenis_install|install Molgenis on Ubuntu]] ?

===== PyMOL =====

  * How do I [[howto:pymol_install_on_windows|install PyMOL on windows]] ?
  * How do I [[howto:pymol_select_by_res_from_obj|select all residues within n distance from an object]] ?


===== RClone =====

  * How do I [[howto:rclone_copy_shared_folder_locally|copy a "shared with me" directory locally]] ?

===== Rocks Cluster =====

This is perhaps the most annoying piece of software I have ever managed.  Questions on the mailing list either go unanswered or else are replied with "//it is easier to just reinstall your cluster//".  I mean, seriously guys.  I am writing these notes down as I am sure I will need to refer to them later.

  * How do I [[howto:rocks_reinstall_compute_node|reinstall a compute node from scratch]]?
  * How do I [[howto:rocks_add_interface|add an interface (e.g. public) to a compute node]]?
  * How do I [[howto:rocks_add_user|add a user to the Rocks cluster]]?
  * How do I [[howto:rocks_distribute_file|distribute a file across all the nodes in the cluster]]?
  * How do I [[howto:rocks_change_private_network_domain_name|change Rocks cluster private domain name]]?
  * How do I [[howto:rocks_install_package_rpm|install an RPM across all compute nodes (on kickstart)]]?
  * How do I [[howto:rocks_create_package_rpm|create an RPM package from an existing directory (how to package a program)]]?
  * How do I [[howto:rocks_ftp_a_file_from_head_to_compute_nodes_on_installation|FTP a file from head to compute nodes on installation]]?
  * How do I [[howto:rocks_configure_the_second_ethernet_card_on_compute_nodes|configure the second ethernet card on compute nodes so that the rest of the intranet (and internet) is available to compute nodes]]?

===== University of Malta =====

  * How do I [[howto:vpn_install_arch|install UM's VPN on Arch Linux]]?

===== Virtual Machines =====

  * How do I [[howto:vm_install_lubuntu|install and run Lubuntu in a Virtual Machine]]?

===== Wordpress =====

  * How do I [[howto:wordpress_reset_theme|reset a theme in Wordpress (like fresh install)]]?