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View Code? Open in Web Editor NEWThings that Need to be done on the HPC.
Things that Need to be done on the HPC.
Hi, kindly help us in installing the following tools required in our min-project:
Thank you,
Here are some of the tools that the HPC users need to have set up in the HPC. If you have some time, please install them.
The packages are DECIPHER and phangorn, which are the packages required for the last step of this pipeline. @espirado, are you around to assist?
We can setup a script that creates user accounts after the user fills the form, and the account is approved. See this resource: https://www.cyberciti.biz/faq/rhel-debian-force-users-to-change-passwords/
Create a shareable file system from the main node to serve as an administrative data access for the other nodes
@- [ ] Server uptime and monitoring
Tools needed to be installed in the galay instance
Tool | Description |
---|---|
bwa_mapper | galaxy BWA short reader aligner |
... | .. |
error while loading shared libraries: libhts.so.2: cannot open shared object file: No such file or directory
@andrew espira
Set up slurm server on the main node and client on worker nodes
Hi Andrew! We can explore using a VM machine as the master for Slurm. Here are some resources that can be useful.
Work around
- Firewall was blocking node communication
use these resources:
The latest server is Ubuntu 18.04 for the HPC. To do this, we must get the following done:
Please assist to install Prinseq and Pear for 16S data analysis on HPC.
Prinseq: https://anaconda.org/bioconda/prinseq
Chimeraslayer : https://www.howtoinstall.me/ubuntu/18-04/chimeraslayer/
Pear: https://anaconda.org/bioconda/pear
At some point, we may explore setting up, and testing moodle for use with ENBiT and our inhouse training. The instalation is not a priority for now, but using this issue to keep track of various resources we can use.
Andrew help with installing RDP on the server. Its GUI based.
Install from http://cab.spbu.ru/software/spades/
Bug on cent os 7 and open access server. Firewall automatically closed all remote access to the system. bug chaser
Status
error while loading shared libraries: libhts.so.2: cannot open shared object file: No such file or directory
error while loading shared libraries: libhts.so.2: cannot open shared object file: No such file or directory
We are having problem running samtools, seems libhts.so.2: library is not available @Espira
For Kennedy's project, he needs to have access to the Cytoscape GUI. One solution he has found is the use of the NoMachine. We can explore how we can set this up in the HPC.
Here is the download site: https://www.nomachine.com/download/linux&id=1
We can settle for Cent Os 7 for compatibility with the existing server. @kipkurui have settled with setting the nodes as a single cluster which can allow access of both from either. A few links on doing that
Setup Two Node Red Hat Cluster without shared storage
How to configure Two Node High Availability Cluster On RHEL/CentOS 7.6
How To Configure High-Availability Cluster on CentOS 7 / RHEL 7
I will try to get a few documentations from the other admins
Globus Connect Personal enables you to share and transfer files to and from your Linux laptop or desktop computer
Get Requirements needs and modules that support the extensive analysis that is being undertaken within the platform
Guides
Galaxy training
Galaxy course
This library seems to be missing or not working on the server. The error is as below;
error while loading shared libraries: libssl.so.1.0.0: cannot open shared object file: No such file or directory
@- [x] Instal RStudio
Documentations and links for how we are preparing our cluster for running the various sequences jobs for 16s
Hi Andrew.
Been testing the Jupyer HUb, and it seems when I create an environment and install packages, they don't seem to be accessible on my notebooks. Any ideas?
PS: Am I still in the sudoers list?
For Advanced H3ABioNet training, we will need to set up Singularity. See this documentation for HPC set up that can be useful here as well. Let's make a plan for setting this up as well.
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