Difference between revisions of "Base software kit"
Jump to navigation
Jump to search
m |
m |
||
| Line 1: | Line 1: | ||
| − | These software packages should be installed on every machine we provision, regardless of their purpose. A script | + | These software packages should be installed on every machine we provision, regardless of their purpose. A script [https://gitlab.cluster.earlham.edu/sysadmin/server-scripts/tree/master 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 | * nano - text editor | ||
* vim - text editor | * vim - text editor | ||
Revision as of 09:12, 4 May 2020
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
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
