Showing below up to 47 results starting with #1.
View (previous 50) (next 50) (20 | 50 | 100 | 250 | 500).
- 01:27, 12 November 2009 Serenity:Installed Applications (hist) [1,611 bytes] Rlyon (Talk | contribs) (New page: ===Base ''(module load base)''=== This is the base systems module. Although it is not required to be loaded, If other modules are loaded without the base module you will lose the man page...)
- 16:55, 26 October 2009 Assistantship: PSES (hist) [2,143 bytes] Celesteb (Talk | contribs) (New page: '''U of I Graduate Assistantship''' An interdisciplinary, Ph.D. graduate student assistantship is available at the University of Idaho. This assistantship will be funded through a joint ...)
- 21:27, 5 October 2009 Tutorial: Queues and backfill scheduling (hist) [4,482 bytes] Rlyon (Talk | contribs) (New page: ==Queues== There are currently several queues on fourtytwo. These queues each have different time limits and priorities that are applied in scheduling your job. To see the queues availa...)
- 20:21, 1 October 2009 Cluster Submit Scripts - Beast (hist) [325 bytes] Rlyon (Talk | contribs) (New page: '''beast.pbs''' #!/bin/sh #PBS -N beast #PBS -j oe #PBS -l nodes=1:ppn=8 . /usr/modules/init/bash module load beast beast $FILE Run as # qsub -v FILE=myfile.xml beast.pbs)
- 00:29, 30 September 2009 Cluster Submit Scripts - R (hist) [196 bytes] Rlyon (Talk | contribs) (New page: '''R.pbs''' #!/bin/sh #PBS -N Rjob #PBS -q short . /usr/modules/init/bash module load R R < $FILE --no-save To submit the file, use the following command: # qsub -v FILE=myfile...)
- 21:24, 15 September 2009 Cluster Submit Scripts - Paup (hist) [106 bytes] Rlyon (Talk | contribs) (New page: #!/bin/sh #PBS -N myname . /usr/modules/init/bash module load paup paup myfile.nex)
- 20:17, 1 September 2009 BCB Courses: 404 (hist) [6,586 bytes] Rlyon (Talk | contribs) (New page: ='''BCB 404 Special Topic:''' '''COMPUTING FOR BIOINFORMATICS'''= This course will teach basic computing skills for biologists and others who are interested in bioinformatics. It is a 4 ...)
- 22:48, 25 June 2009 Logos (hist) [503 bytes] Cblair (Talk | contribs) (New page: thumb thumb thumb thumb thumb [[Image:INBRElog...)
- 21:51, 24 June 2009 Cluster Administration - Installing a Linux PPC Cluster (hist) [3,245 bytes] Rlyon (Talk | contribs) (New page: = Headnode Operating System Install = After trying out several Linux variants I settled on Fedora 10. Mostly because of the Yum package manager and that it behaves more closely with the C...)
- 21:44, 23 June 2009 Servers (hist) [49 bytes] Tnelson (Talk | contribs) (New page: This is a page for the future server description.)
- 00:46, 17 June 2009 Cluster Submit Scripts - Garli (Garli - MPI version) (hist) [396 bytes] Rlyon (Talk | contribs) (New page: ====garli.pbs==== #!/bin/sh #PBS -l nodes=4 # Initialize and load the modules . /usr/modules/init/bash module load openmpi # Move to the working directory. Garli.conf must be #...)
- 19:58, 16 June 2009 Cluster Submit Scripts - PaCE (PaCE) (hist) [1,564 bytes] Rlyon (Talk | contribs) (New page: To run PaCE on a pbs based system use the following script: #!/bin/sh # Lets use four processors on four seperate nodes. See the qsub # tutorials for information on how to use multip...)
- 04:41, 28 May 2009 Cluster Submit Scripts - Blastp2tree (hist) [2,273 bytes] Rlyon (Talk | contribs) (New page: ==Description== Blastp2tree is a series of scripts designed to run on a PBS based cluster. It requires mpiblast, ncbitools, clustalw-mpi, and raxmlHPC-MPI. ==Instructions== To run blastp...)
- 22:32, 27 May 2009 Cluster Submit Scripts - clustalw-mpi (clustalw-mpi) (hist) [300 bytes] Celesteb (Talk | contribs) (New page: #PBS -l nodes=1:ppn=5 #PBS -M celesteb@uidaho.edu #PBS -m abe . /usr/modules/init/bash module load openmpi mpirun clustalw-mpi $file -outfile=$file.aln -type=protein -align)
- 19:11, 27 May 2009 Solution: Using mpiBLAST - Exercise 1 (hist) [890 bytes] Rlyon (Talk | contribs) (New page: This is a possible solution to the exercise ==mpiblast.wrap== #!/bin/sh # Did we get 2 arguments? if [ $# -ne 2 ] ; then echo "WRONG! $0 takes 2 arguments." exit 1...)
- 15:28, 27 May 2009 Tutorial: Submitting parallel jobs (hist) [1,706 bytes] Rlyon (Talk | contribs) (New page: ==Differences between parallel applications and sequential or serial applications== To be finished at a later time. Forms of parallel computing. * Bit level * Instruction level * Data...)
- 14:40, 26 May 2009 Tutorial: Distributing a task to nodes (non-parallel) (hist) [1,658 bytes] Rlyon (Talk | contribs) (New page: Often it is necessary to have tasks run in parallel without using MPI. Torque provides a tool called pbsdsh to facilitate this. This application is run from your submission script and sp...)
- 05:14, 26 May 2009 Tutorial: Removing a job from the cluster (hist) [1,468 bytes] Rlyon (Talk | contribs) (New page: You may remove a job at anytime from the cluster by using the qdel command. The qdel command takes one argument which is the id number of the job that you are wishing to remove. ====Try i...)
- 04:58, 26 May 2009 Tutorial: Viewing the output of a running job (hist) [945 bytes] Rlyon (Talk | contribs) (New page: ''back to Clusters'' ==Using qpeek== By default the job output is stored on the execution node until the job is complete. Once complete it is copied to the appropriate default locatio...)
- 04:14, 26 May 2009 Tutorial: Check on the status of the cluster or all your jobs (hist) [7,352 bytes] Rlyon (Talk | contribs) (New page: There are several tools available to check on different aspects of the cluster. The qstat, showq, and qnodes tools are the primary tools used to get the status of the batch server, cluste...)
- 01:14, 26 May 2009 Tutorial: Interactive jobs (hist) [132 bytes] Rlyon (Talk | contribs) (New page: ==Asking qsub for an interactive job== ==Exercises== 1. Create an alias to run an interactive mrbayes job.)
- 00:44, 26 May 2009 Tutorials: Your home directory (hist) [1,402 bytes] Rlyon (Talk | contribs) (New page: ''back to Clusters'' ==What is your home directory== Your home directory is a place for you to store all your files and data related to your research. On the clusters, this home direc...)
- 00:24, 26 May 2009 Tutorials: Where am I? (hist) [2,136 bytes] Rlyon (Talk | contribs) (New page: ==So, now that I am logged in to a cluster, where exactly am I?== Once you are logged into a cluster, you are on a machine which is referred to as the 'headnode' or the '[[headnode|mas...)
- 23:43, 25 May 2009 Tutorials: Logging in for the first time (hist) [4,904 bytes] Rlyon (Talk | contribs) (New page: ===Protocols supported for logging in=== For first time login, only the ssh protocol is supported. ====SSH==== The (S)ecure (SH)ell protocol opens up a pseudo terminal connection, which wi...)
- 22:18, 23 May 2009 Tutorials: Loading modules at login (hist) [834 bytes] Rlyon (Talk | contribs) (New page: ==Autoload Environment Modules on Login== Assuming that you are using the default bash shell on our systems, create/edit a file called '''.bashrc'''. If you are using another shell creat...)
- 22:10, 23 May 2009 Tutorials: Creating your own modulefiles (hist) [1,730 bytes] Rlyon (Talk | contribs) (New page: ===Creating your own modulefile=== You can customize your own environment by creating and loading your own modulefiles. To use your own modulefiles you must first create a directory for ...)
- 22:07, 23 May 2009 Tutorials: Using modules to load applications (hist) [4,650 bytes] Rlyon (Talk | contribs) (New page: ''Back to Clusters'' ==Description== "The Environment Modules package provides for the dynamic modification of a user's environment via modulefiles. Each modulefile contains the inf...)
- 21:00, 21 May 2009 Tutorial: Submitting a job using qsub (hist) [11,794 bytes] Rlyon (Talk | contribs) (New page: ==What is qsub?== Qsub is the command used for job submission to the cluster. It takes several command line augments and can also use special directives found in the submission scripts or...)
- 18:58, 13 May 2009 Schedule (hist) [462 bytes] Celesteb (Talk | contribs) (New page: {| class="Schedule" |- ! Topic ! Lecture ! Exercises |- | IBEST Core facilities | Mon AM |- | Unix environment||Mon AM||Mon PM |- | Shell scripting||Tues AM||Tues AM | row 2, cell 3 |} Top...)
- 16:13, 28 April 2009 Fourtytwo:Installed Applications (hist) [4,751 bytes] Rlyon (Talk | contribs) (New page: ===Base ''(module load base)''=== This is the base systems module. Although it is not required to be loaded, If other modules are loaded without the base module you will lose the man page...)
- 19:25, 21 April 2009 Darwin: Using the Roche GS Tools (hist) [22 bytes] Rlyon (Talk | contribs) (New page: ==Using the GS Tools==)
- 16:59, 2 April 2009 IBEST Website (hist) [9,587 bytes] Cblair (Talk | contribs) (New page: ==IBEST Website== This page is dedicated to the development and maintenance of the IBEST Website. During development, I have been using other pages to keep my development notes, but it on...)
- 19:53, 20 January 2009 Citations (hist) [1,174 bytes] Celesteb (Talk | contribs) (New page: How to cite the agencies that fund the resources that are available through IBEST If you use the IBEST facilities to generate data for a paper, poster, or grant application, you should re...)
- 19:26, 20 January 2009 Where (hist) [3,844 bytes] Ally (Talk | contribs) (New page: Example for posting a link. Kneitel & Chase (2004) Trade-offs in community ecology: linking spatial scales and species coexistence. Ecology Letters 7: 69-80. [[http://www3.interscience....)
- 19:36, 15 January 2009 Bioinformatics Core Description (hist) [6,087 bytes] Rlyon (Talk | contribs) (New page: ==Short Summary== Bioinformatics Core – Four compute clusters: 512 core AMD64 primary production system; 96 processor Intel Xeon secondary production system; 96 processor PowerPC G5 te...)
- 18:45, 15 January 2009 IBEST Lunch (hist) [1,518 bytes] Cblair (Talk | contribs) (New page: == 2009 Schedule == {{Shortbox |January 15th, 2009 | *Speaker: Robert Lyon *Location: Aurora Room (4th floor of the Commons) *Time: 12:30pm }})
- 20:00, 14 January 2009 Pico (hist) [429 bytes] Cblair (Talk | contribs) (New page: Pico is a shell or command line text editor. It will already be installed on the computer or terminal you are trying to use if the system allows it to be usable, and can be accessed by typ...)
- 19:53, 14 January 2009 Emacs (hist) [369 bytes] Cblair (Talk | contribs) (New page: Emacs is a text editing program used from a shell or command prompt line. It is similar to Nano == External Links == * [http://en.wikipedia.org/wiki/GNU_Emacs Wikipedia Emacs Ar...)
- 18:42, 14 January 2009 GeneSpring (hist) [423 bytes] Cblair (Talk | contribs) (New page: GeneSpring is an analysis platform that provides "comprehensive statistical analysis, data mining, and visualization tools" for broad types of research, usually biological.<ref>[http://www...)
- 00:30, 14 January 2009 Matlab (hist) [157 bytes] Cblair (Talk | contribs) (New page: Matlab is a programming language for numerical computing in a shell or command prompt environment. For the full wiki, see <a href="http://en.wikipedia.org/wiki/Matlab">Mathlab Wikipedia</a...)
- 00:01, 9 January 2009 Software (hist) [1,374 bytes] Rlyon (Talk | contribs) (New page: =Software on the IBEST systems= RAxML RepBase RepeatMasker concaterpillar Phred/Phrap/Consed Lamarc MrBayes R8 Muscle Clustalw Clustalx Cutg Emboss HMMER NCBI Toolkit Paml Phylip Phyml Re...)
- 19:26, 17 December 2008 Scripts (hist) [5,071 bytes] Foster (Talk | contribs) (New page: ==scripts== ===strip_OTUs=== <pre> #!/usr/bin/perl # selects the first member of a list of OTU equivalences (from dotur), x.fn.list # # syntax: strip_OTUs fn # # input (in file "fn", on...)
- 19:05, 17 December 2008 454 community metagenomic (16S) analysis (hist) [6,070 bytes] Foster (Talk | contribs) (New page: ==align the sequences== I prefer to use the RDP aligner in the pyro pipeline, which is aware of secondary structure and can handle large volumes of data::http://pyro.cme.msu.edu/pyro Note...)
- 18:30, 17 December 2008 Howto (hist) [3,916 bytes] Foster (Talk | contribs) (New page: ===pbs=== To learn how to use pbs, go here (PBS). Or, better yet, ask someone who has done it to show you! ===work with multiple files=== When you log on to Unix, you are actually r...)
- 17:19, 17 December 2008 How I learned this (hist) [85 bytes] Foster (Talk | contribs) (New page: == Portable Batch Processing (PBS) == To learn about PBS, I read the IBEST wiki!)
- 19:03, 16 December 2008 Rnj (hist) [378 bytes] Foster (Talk | contribs) (New page: == Relaxed Neighbor Joining == Relaxed Neighbor Joining is the fastest existing algorithm for creating a "neighbor joining" tree from a distance matrix. The algorithm actually relaxes a c...)
- 19:00, 16 December 2008 Reorganize the data (hist) [2,260 bytes] Foster (Talk | contribs) (New page: I chose a directory structure and file name convention that made the following clear: * what analysis I was running (for example, analysis by age of the sample, or by individual sample) * ...)
