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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.  
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This wiki has moved! this page is here merely for archival reasons.
  
*If you want to be able to edit the wiki, let us know and we'll add you to the list of contributors.
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[https://github.com/uio-cees/hpc/wiki '''Visit the new wiki here''']
*If you add a page, please list it below! [[Tips for adding a page|Tips for adding a page]].<br>
 
  
<br>
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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.
  
== Mailing lists  ==
+
*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]].
  
*'''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/bio.uio.no/subscribe/cees-hpc Subscribe here].
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== Compute resources ==
*'''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'&nbsp;:-) USIT will also send emails to that list when discs on the nodes are full etc. [https://sympa.uio.no/bio.uio.no/subscribe/cod-nodes Subscribe here].
 
*'''cees-bioinf''': to be used for general information regarding bioinformatics at CEES. [https://sympa.uio.no/bio.uio.no/subscribe/cees-bioinf Subscribe here].
 
  
<br>
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=== Overview ===
  
<br>
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We have a mix of self-owned compute hardware and disk space, rented disk space, supplemented with an allocation on the UiO supercomputer 'Abel'.&nbsp;<br />For details, see
  
== Use of the CEES hardware and Abel<br>  ==
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*[[User_manual_cod_nodes|User manual cod nodes]]
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*[[Abel_use|Abel use]]
  
[[User manual cod nodes|User manual cod nodes]]
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=== Getting access ===
  
[[Abel use|Abel use]]
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Please fill out this form:&nbsp;https://nettskjema.uio.no/answer/64174.html
  
[[Organising your work|Organising your computational work]]
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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
  
[[Useful websites with Unix commands|Useful websites with Unix commands]]
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=== Yearly reports ===
  
<br>
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We write a yearly report on the resources and bioinformatic activities at CEES. See the [[Yearly reports|yearly reports page]].
  
== How-to's  ==
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== Use of the CEES hardware and Abel ==
  
[[PacBio smrtpipe commandline|PacBio smrtpipe command-line use]]  
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[[User manual cod nodes|User manual cod nodes]]
  
[[Submitting to ENA|Submitting sequences to ENA]]  
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[[Abel use|Abel use]]
  
[[Check insert size distribution new sequencing library|Quickly check the insert size distribution of a new sequencing library]]  
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[[Software and modules|Installing software and creating modules]]
  
[[Error correction of Illumina reads using Celera Assembler|Error correction of Illumina reads using merTrim from the Celera Assembler package]]  
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[[Variant calling on Abel]]
  
[[Assembly of Illumina paired end reads using Celera Assembler]]
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[[Sliding_window_analyses_with_vcf_files|Sliding window analyses with vcf files]]
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== 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]]
 +
 
 +
[[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&nbsp;virtualenv on the nodes]]
 +
 
 +
[[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'&nbsp;:-) 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 09:38, 21 November 2017

This wiki has moved! this page is here merely for archival reasons.

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.

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

User manual cod nodes

Abel use

Installing software and creating modules

Variant calling on Abel

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

Submitting sequences to ENA

Using virtualenv on the nodes

Quickly check the insert size distribution of a new sequencing library

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. 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.