Base software kit

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
• 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

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 phat node, 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