Difference between revisions of "Base software kit"
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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). | 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). | ||
| + | |||
| + | These are done in a playbook now, see the sysadmin/Ansible-Playbooks project in GitLab: | ||
* nano - text editor | * nano - text editor | ||
* vim - text editor | * vim - text editor | ||
| Line 9: | Line 11: | ||
* gcc - most recent C compiler (modules can support as many versions as we'd like but we need at least one) | * 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 | * ntp - get a time server | ||
| − | * | + | * mlocate |
* rsync | * rsync | ||
| − | + | * strace | |
| − | + | * zsh | |
| − | * | + | * curl |
| + | * rclone | ||
* openldap | * openldap | ||
* openldap-clients | * openldap-clients | ||
* openssh-ldap | * openssh-ldap | ||
| − | * pam_ldap | + | * pam_ldap or libpam-ldap |
* nss-pam-ldapd | * nss-pam-ldapd | ||
| + | * unattended-upgrades or yum-conf or dnf-automatic (also configure to automatically apply security patches) | ||
| − | On a | + | Do these manually (or expand the playbook): |
| − | * | + | * Install Nagios |
| + | * modules | ||
| + | * LDAP client | ||
| + | |||
| + | On a high-performance computing server or cluster, add these: | ||
| + | * C3 tools (see [[Sysadmin:C3|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: | ||
* [[Sysadmin:Bioinformatics Packages|ea-utils]] | * [[Sysadmin:Bioinformatics Packages|ea-utils]] | ||
* [[Sysadmin:Bioinformatics Packages|AdapterRemoval]] | * [[Sysadmin:Bioinformatics Packages|AdapterRemoval]] | ||
| Line 32: | Line 45: | ||
* PMD tools | * PMD tools | ||
* mapdamage2 | * mapdamage2 | ||
| + | |||
| + | If the server will host surveying software, add these: | ||
| + | * Docker | ||
| + | * ODM | ||
| + | * WebODM | ||
Python libraries (Python 3): | Python libraries (Python 3): | ||
Latest revision as of 12:43, 14 January 2021
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).
These are done in a playbook now, see the sysadmin/Ansible-Playbooks project in GitLab:
- 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
- mlocate
- rsync
- strace
- zsh
- curl
- rclone
- openldap
- openldap-clients
- openssh-ldap
- pam_ldap or libpam-ldap
- nss-pam-ldapd
- unattended-upgrades or yum-conf or dnf-automatic (also configure to automatically apply security patches)
Do these manually (or expand the playbook):
- Install Nagios
- modules
- LDAP client
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
