ILRI Research Computing

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====== ILRI Research Computing ======
This is the ILRI Research Computing wiki.  Here you'll find information about all aspects of the research computing infrastructure, including tutorials and usage information for users.  Please use this wiki to document all changes you make to servers, services, and applications.

===== Servers =====
[[servers|List of servers at ILRI]]

===== Software =====

[[software|Software resources]] at ILRI, broken up into loosely-related areas:

  * [[software:programming|Programming and scripting]]
  * [[software:statistics|Statistics]]
  * [[software:scheduling|Scheduling]] -- software for managing cluster resources
  * [[software:genome_assembly|Genome Assembly]]
  * [[software:alignment|Alignment]]
  * [[software:metagenomics|Metagenomics]]
  * [[software:webservers|Web servers]]
  * [[software:internal:sysadmin|Systems administration]]

To move/reorganize:
  * Configure [[idea|IDEA]]
  * [[pasa|PASA]] web interface
  * [[WebLab]]
  * [[openmpi|OpenMPI]]
  * [[PPP|Pathogen Profiling Pipeline]]
  * [[Interproscan]]
  * [[ergatis]]
  * [[workflow engine|Installing Workflow Engine]]
  * [[samba|Configuring Samba]] for Windows filesharing
  * [[genvar]], a pipeline designed to analyze an annotated genome
  * [[Bio::Tools::CodonOptTable]]
  * Install [[PSPP]]
  * [[form_tools|Form Tools]]: Automated form processing and reporting
  * Install [[Mobyle]]
  * Install [[DIY]] -> Do-It-Yourself! Annotator
  * [[server_monitoring|Server monitoring]] tools
  * [[Chado]], the relational database schema
  * [[AMOS]], infrastructure for developing assembly tools
  * [[WindowMasker]], identify and mask repetitive DNA sequences in a genome
  * [[RepeatMasker]], screen DNA sequences for interspersed repeats and low complexity DNA sequences
  * [[GAAS]], calculate accurate community composition and average genome size in metagenomes by using BLAST, advanced parsing of hits and correction of genome length bias
  * [[Bio-Linux]], a Ubuntu derivative with common Bioinformatics tools
  * [[SeqClean:seqclean|seqclean]], a script for automated trimming and validation of ESTs or other DNA sequences by screening for various contaminants, low quality and low-complexity sequences.
  * [[ldap_integration|Active Directory integration]] (for ssh logins using CGIAR-wide AD credentials)
  * [[Tech Recipes]]
  * [[Installing Gbrowse2]]
  * [[Uninstalling Perl Modules]]
  * [[Monitoring]]

===== Hardware =====
  * [[RAID]] on HPC
  * [[backup|Backups]]
  * [[apcupsd]] - Auto-shutdown on power failure using acupsd

===== Brainstorms =====
Notes from various group brainstorm sessions.
  * [[brainstorms|Brainstorming]]

====== Tips and tricks ======
  * [[shell_tips|Shell tips and tricks]]
  * [[perl|Perl]] tips
  * [[rocks_commands|Rocks commands]]
  * [[FreeBSD]] tips
  * [[RPM]] tips
  * [[virtualbox|VirtualBox]] tips
  * [[Kernel compiling]]
  * [[HPC concepts]]
  * [[Database]]
  * [[Project management]]
  * Using [[Diskutil|Diskutil.app]] (Mac OS X only)
  * Working with [[Java jar files]]
  

====== Contact ======

E-mail questions, comments, or corrections to the maintainers of this wiki:
  * [[wiki:user:aorth|Alan Orth]]: a.orth@cgiar.org
  * [[wiki:user:ikahugu|Isaac Kahugu]]: i.kahugu@cgiar.org