Base software kit

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Revision as of 10:59, 21 May 2020 by Craigje (talk | contribs)
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These software packages should be installed on every machine we provision, regardless of their purpose. A script on GitLab has a dirt-simple script to do this, though it should be improved and/or developed (including making an Ansible playbook for easy install on a bunch of cluster nodes).

  • nano - text editor
  • vim - text editor
  • emacs - text editor
  • nfs-common for Debian or nfs-utils for CentOS - allow NFS mounts
  • wget - wget a file from the Internet
  • iproute2 - more modern instantiations of ifconfig and a lot of other network tools
    • net-tools for those among us who like ifconfig
  • gcc - most recent C compiler (modules can support as many versions as we'd like but we need at least one)
  • ntp - get a time server
  • modules
  • rsync
  • rclone
  • openldap
  • openldap-clients
  • openssh-ldap
  • pam_ldap
  • nss-pam-ldapd
  • unattended-upgrades or yum-conf or dnf-automatic (also configure to automatically apply security patches)

On a high-performance computing server or cluster, add these:

  • C3 tools (see the C3 tools page) - possibly deprecated, Ansible is a good replacement
  • Slurm
  • OpenMPI (latest version)

If the server will be used for bioinformatics, add these:

  • ea-utils
  • AdapterRemoval
  • sga
  • BBMapTool
  • bowtie2
  • samtools
  • NCBI mitochondrial and plastid databases (full URLs, they’re stable)
  • Python scripts to subset databases and SAM files by species
  • PMD tools
  • mapdamage2

If the server will host surveying software, add these:

  • Docker
  • ODM
  • WebODM

Python libraries (Python 3):

  • Pandas
  • Numpy
  • Scipy