Difference between revisions of "Old Main Page"
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− | This wiki is | + | This wiki has moved! this page is here merely for archival reasons. |
− | + | [https://github.com/uio-cees/hpc/wiki '''Visit the new wiki here'''] | |
− | |||
− | + | This wiki is meant as a repository for bioinformatical knowledge at the CEES. It is mainly run by Lex, but others are also very welcome to contribute. | |
− | + | *If you want to be able to edit the wiki, let us know and we'll add you to the list of contributors. | |
+ | *If you add a page, please list it below! [[Tips for adding a page|Tips for adding a page]]. | ||
− | + | == Compute resources == | |
− | |||
− | |||
− | |||
− | + | === Overview === | |
− | + | We have a mix of self-owned compute hardware and disk space, rented disk space, supplemented with an allocation on the UiO supercomputer 'Abel'. <br />For details, see | |
− | [[User manual cod nodes| | + | *[[User_manual_cod_nodes|User manual cod nodes]] |
+ | *[[Abel_use|Abel use]] | ||
− | + | === Getting access === | |
− | [[ | + | Please fill out this form: https://nettskjema.uio.no/answer/64174.html |
+ | |||
+ | NOTE '''Non-UiO staff''': you will need a guest researcher account. Your collaborator from UiO will need to submit application for this, see http://www.uio.no/english/for-employees/support/human-resources/payroll/hr-payrollsystem/associated-users.html | ||
+ | |||
+ | === Yearly reports === | ||
+ | |||
+ | We write a yearly report on the resources and bioinformatic activities at CEES. See the [[Yearly reports|yearly reports page]]. | ||
+ | |||
+ | == Use of the CEES hardware and Abel == | ||
+ | |||
+ | [[User manual cod nodes|User manual cod nodes]] | ||
+ | |||
+ | [[Abel use|Abel use]] | ||
+ | |||
+ | [[Software and modules|Installing software and creating modules]] | ||
[[Variant calling on Abel]] | [[Variant calling on Abel]] | ||
− | + | [[Sliding_window_analyses_with_vcf_files|Sliding window analyses with vcf files]] | |
== Tips, tricks, useful links == | == Tips, tricks, useful links == | ||
+ | |||
+ | [https://github.com/uio-cees/hpc/wiki/Frequently-Asked-Questions-(FAQ) Check out the FAQ (work in progress)] | ||
[[Organising your work|Organising your computational work]] | [[Organising your work|Organising your computational work]] | ||
Line 33: | Line 47: | ||
[[Useful websites with Unix commands|Useful websites with Unix commands]] | [[Useful websites with Unix commands|Useful websites with Unix commands]] | ||
− | [[ | + | [[Useful websites with Python|Useful websites with Python tips and tricks]] |
+ | |||
+ | [[Useful websites with R|Useful websites with R tips and tricks]] | ||
+ | |||
+ | [[Usefull small commands scripts etc|Useful small commands/scripts etc in /projects/cees]] | ||
+ | |||
+ | [[Using mosh to avoid losing ssh connections]] | ||
+ | |||
+ | == How-to's == | ||
− | + | [[PacBio smrtpipe commandline|PacBio smrtpipe command-line use]] | |
− | [[ | + | [[Submitting to ENA|Submitting sequences to ENA]] |
− | [[ | + | [[Using virtualenv|Using virtualenv on the nodes]] |
− | [[Check insert size distribution new sequencing library|Quickly check the insert size distribution of a new sequencing library]] | + | [[Check insert size distribution new sequencing library|Quickly check the insert size distribution of a new sequencing library]] |
− | [[ | + | [[Using PBHoney|Using PBHoney]] |
− | + | == Mailing lists == | |
− | [[ | + | *'''cees-hpc''': to be used for general information related to the area under /projects/cees, the able CPUs and the cod-nodes. [https://sympa.uio.no/ibv.uio.no/subscribe/cees-hpc Subscribe here]. |
+ | *'''cod-nodes''': to be used to inform about the other cod-node users about CPUs and memory usage of the cod nodes, aka 'cod-node hugging' :-) USIT will also send emails to that list when discs on the nodes are full etc. [https://sympa.uio.no/ibv.uio.no/subscribe/cod-nodes Subscribe here]. | ||
+ | *'''cees-bioinf''': to be used for general information regarding bioinformatics at CEES. [https://sympa.uio.no/ibv.uio.no/subscribe/cees-bioinf Subscribe here]. |
Latest revision as of 10:38, 21 November 2017
This wiki has moved! this page is here merely for archival reasons.
This wiki is meant as a repository for bioinformatical knowledge at the CEES. It is mainly run by Lex, but others are also very welcome to contribute.
- If you want to be able to edit the wiki, let us know and we'll add you to the list of contributors.
- If you add a page, please list it below! Tips for adding a page.
Contents
Compute resources
Overview
We have a mix of self-owned compute hardware and disk space, rented disk space, supplemented with an allocation on the UiO supercomputer 'Abel'.
For details, see
Getting access
Please fill out this form: https://nettskjema.uio.no/answer/64174.html
NOTE Non-UiO staff: you will need a guest researcher account. Your collaborator from UiO will need to submit application for this, see http://www.uio.no/english/for-employees/support/human-resources/payroll/hr-payrollsystem/associated-users.html
Yearly reports
We write a yearly report on the resources and bioinformatic activities at CEES. See the yearly reports page.
Use of the CEES hardware and Abel
Installing software and creating modules
Sliding window analyses with vcf files
Tips, tricks, useful links
Check out the FAQ (work in progress)
Organising your computational work
Useful websites with Unix commands
Useful websites with Python tips and tricks
Useful websites with R tips and tricks
Useful small commands/scripts etc in /projects/cees
Using mosh to avoid losing ssh connections
How-to's
PacBio smrtpipe command-line use
Quickly check the insert size distribution of a new sequencing library
Mailing lists
- cees-hpc: to be used for general information related to the area under /projects/cees, the able CPUs and the cod-nodes. Subscribe here.
- cod-nodes: to be used to inform about the other cod-node users about CPUs and memory usage of the cod nodes, aka 'cod-node hugging' :-) USIT will also send emails to that list when discs on the nodes are full etc. Subscribe here.
- cees-bioinf: to be used for general information regarding bioinformatics at CEES. Subscribe here.