Base software kit

From Earlham CS Department
Revision as of 09:37, 9 March 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 in /root/install on tools has a model for a dirt-simple script to do this, though it could probably be improved and/or developed into an Ansible playbook.

  • 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

On a cluster, add these:

  • C3 tools (see the C3 tools page) - possibly deprecated, Ansible is a good replacement
  • openldap
  • openldap-clients
  • openssh-ldap
  • pam_ldap
  • nss-pam-ldapd

On a jumbo server, add these:

  • rclone
  • 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

Python libraries (Python 3):

  • Pandas
  • Numpy
  • Scipy