Difference between revisions of "Base software kit"
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* nano - text editor | * nano - text editor | ||
* vim - text editor | * vim - text editor | ||
| + | * emacs - text editor | ||
* nfs-common for Debian or nfs-utils for CentOS - allow NFS mounts | * nfs-common for Debian or nfs-utils for CentOS - allow NFS mounts | ||
* wget - wget a file from the Internet | * wget - wget a file from the Internet | ||
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* nss-pam-ldapd | * nss-pam-ldapd | ||
| − | On a | + | On a jumbo server, add these: |
* rclone | * rclone | ||
* [[Sysadmin:Bioinformatics Packages|ea-utils]] | * [[Sysadmin:Bioinformatics Packages|ea-utils]] | ||
Revision as of 10:54, 18 February 2020
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
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
