Recent Changes

Wednesday, March 5

  1. page Torque edited ... /var/spool/torque/spool/[job id].localhost.OU /var/spool/torque/spool/[job id].localhost.ER …
    ...
    /var/spool/torque/spool/[job id].localhost.OU
    /var/spool/torque/spool/[job id].localhost.ER
    ...
    described above. After completion, these files will be moved to the directory from which the job was started (or where specified if #PBS -o and #PBS -e were used).
    Changing the configuration of a job already running
    The command to change an existing job configuration is qalter. You should first run qstat to find the job ID. Then run the appropriate qalter command. For example:
    (view changes)
    12:27 pm
  2. page Torque edited ... which will give you a lot more information. Before the job completes, the standard out and st…
    ...
    which will give you a lot more information.
    Before the job completes, the standard out and standard error files, respectively, are located here:
    /var/spool/torque/spool/[job id].OUid].localhost.OU
    /var/spool/torque/spool/[job id].ERid].localhost.ER
    Job ID
    ...
    described above.
    Changing the configuration of a job already running
    The command to change an existing job configuration is qalter. You should first run qstat to find the job ID. Then run the appropriate qalter command. For example:
    (view changes)
    12:25 pm
  3. page Torque edited ... TORQUE resource manager When to use TORQUE ... any management. Purpose of using a reso…
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    TORQUE resource manager
    When to use TORQUE
    ...
    any management.
    Purpose of using a resource manager
    ...
    undetermined time.
    Overview of how TORQUE works
    A job is submitted using the command 'qsub' and a (short) script
    ...
    #PBS -e fileName denotes the location to pipe standard error
    #PBS -d directory changes the default working directory (can also be done using cd in the script as in the example)
    Example script
    Here is an example of doing a Bowtie2 alignment:
    #PBS -l nodes=1:ppn=25,mem=40g,walltime=96:00:00
    ...
    allFastq=$(sed 's/ /,/g' <<< $allFastq)
    bowtie2 -a -p 25 -x $IDX -U $allFastq | samtools view -Sb - > $DIR/$OUT.bam
    ...
    96 hours.
    There are some comments about variables. Notice that they are used within the code, but never set. These variables are set during the qsub command execution.
    ...
    normally would.
    You could save this code in a file, say bowtie2.sh and then run your qsub command:
    qsub -v DIR=/home/pimentel/rawReads/,FASTQ=exp1,IDX=/home/pimentel/bwt2_idx/ensembl-human,OUT=alignments bowtie2.sh
    ...
    $ export OUT=alignments
    $ qsub bowtie2.sh
    ...
    to test.
    If you are running several alignments, this could be useful as you will likely be using the same OUT and IDX names, and just need to change DIR and FASTQ.
    This will find all exp1*.fastq files in /home/pimentel/rawReads, map them against the bowtie index ensembl-human* and name the file alignments.bam in the rawReads directory
    ...
    #PBS -e /place/to/standard/error
    #PBS -o /place/to/standard/out
    ...
    a job
    You can check the status of a job with the qstat command.
    My favorite quick check is the command
    ...
    qstat -f
    which will give you a lot more information.
    ChangingBefore the job completes, the standard out and standard error files, respectively, are located here:
    /var/spool/torque/spool/[job id].OU
    /var/spool/torque/spool/[job id].ER
    Job ID can be found using qstat as described above.
    Changing
    the configuration
    ...
    already running
    The command to change an existing job configuration is qalter. You should first run qstat to find the job ID. Then run the appropriate qalter command. For example:
    qalter 2899.localhost -l walltime=40:00:00,ppn=3
    (view changes)
    12:24 pm

Thursday, November 7

  1. page Factor Association Analyisis MiniGroup edited Some notes, by Saheli, to get you going: My eavesdropping makes me think some of you are wonderin…
    Some notes, by Saheli, to get you going:
    My eavesdropping makes me think some of you are wondering about the kinds of multi-type-data-structures your graphical model can and cannot handle. Could this preprint be helpful? Submitted to the archive on Nov 1, 2013:
    http://arxiv.org/abs/1311.0085
    "We consider the problem of estimating a pairwise graphical model in which the nodes are of different types. In particular, we assume that each node, conditioned on all other nodes, has a distribution that is in the exponential family. To begin, we identify restrictions on the parameter space required for the existence of a well-defined joint density in this setting. Next we establish the consistency of the neighbourhood selection approach for graph reconstruction in high dimensions when the true underlying graph is sparse. Motivated by our theoretical results, we investigate the selection of edges between nodes of two different types, and show that efficiency can be gained if edge estimates obtained from the regressions of particular node types are used to reconstruct the graph. These results are illustrated with examples of Gaussian, binary, Poisson and exponential distributions. Our theoretical findings are corroborated by evidence from simulation studies. We apply the proposed method and competing approaches to a yeast eQTL data set consisting of gene expression and DNA sequence data."
    Thoughts?? Have at it below!!! Don't be afraid to say it's totally useless!!-- Cheers, Saheli

    Stay in touch, Fabulous Five! -- Saheli
    {http://nelsch.org.uk/solveit/images/pentagon2.gif} Let this be your mnemonic for keeping track of each other's well being, progress and needs!
    (view changes)
    2:36 pm
  2. page Factor Association Analyisis MiniGroup edited ... you going: My eavesdropping makes me think some of you are wondering about the kinds of m…
    ...
    you going:
    My eavesdropping makes me think some of you are wondering about the kinds of multi-type-data-structures your graphical model can and cannot handle. Could this preprint be helpful? Submitted to the archive on Nov 1, 2013:
    http://arxiv.org/abs/1311.0085
    "We consider the problem of estimating a pairwise graphical model in which the nodes are of different types. In particular, we assume that each node, conditioned on all other nodes, has a distribution that is in the exponential family. To begin, we identify restrictions on the parameter space required for the existence of a well-defined joint density in this setting. Next we establish the consistency of the neighbourhood selection approach for graph reconstruction in high dimensions when the true underlying graph is sparse. Motivated by our theoretical results, we investigate the selection of edges between nodes of two different types, and show that efficiency can be gained if edge estimates obtained from the regressions of particular node types are used to reconstruct the graph. These results are illustrated with examples of Gaussian, binary, Poisson and exponential distributions. Our theoretical findings are corroborated by evidence from simulation studies. We apply the proposed method and competing approaches to a yeast eQTL data set consisting of gene expression and DNA sequence data."
    ...
    it below!!! --Don't be afraid to say it's totally useless!!-- Cheers, Saheli
    Stay in touch, Fabulous Five! -- Saheli
    {http://nelsch.org.uk/solveit/images/pentagon2.gif} Let this be your mnemonic for keeping track of each other's well being, progress and needs!
    (view changes)
    1:21 pm
  3. page Factor Association Analyisis MiniGroup edited Some notes, by Saheli, to get you going: My eavesdropping makes me think some of you are wonderi…
    Some notes, by Saheli, to get you going:
    My eavesdropping makes me think some of you are wondering about the kinds of multi-type-data-structures your graphical model can and cannot handle. Could this preprint be helpful? Submitted to the archive on Nov 1, 2013:
    http://arxiv.org/abs/1311.0085
    "We consider the problem of estimating a pairwise graphical model in which the nodes are of different types. In particular, we assume that each node, conditioned on all other nodes, has a distribution that is in the exponential family. To begin, we identify restrictions on the parameter space required for the existence of a well-defined joint density in this setting. Next we establish the consistency of the neighbourhood selection approach for graph reconstruction in high dimensions when the true underlying graph is sparse. Motivated by our theoretical results, we investigate the selection of edges between nodes of two different types, and show that efficiency can be gained if edge estimates obtained from the regressions of particular node types are used to reconstruct the graph. These results are illustrated with examples of Gaussian, binary, Poisson and exponential distributions. Our theoretical findings are corroborated by evidence from simulation studies. We apply the proposed method and competing approaches to a yeast eQTL data set consisting of gene expression and DNA sequence data."
    Thoughts?? Have at it below!!! -- Cheers, Saheli

    Stay in touch, Fabulous Five! -- Saheli
    {http://nelsch.org.uk/solveit/images/pentagon2.gif} Let this be your mnemonic for keeping track of each other's well being, progress and needs!
    (view changes)
    12:59 pm

Wednesday, October 23

  1. page Factor Association Analyisis MiniGroup edited Stay in touch, Fabulous Five! -- Saheli {http://nelsch.org.uk/solveit/images/pentagon2.gif} Let t…
    Stay in touch, Fabulous Five! -- Saheli
    {http://nelsch.org.uk/solveit/images/pentagon2.gif} Let this be your mnemonic for keeping track of each other's well being, progress and needs!

    (view changes)
    4:54 pm

Wednesday, September 25

  1. page Peer Review Solicitations Work Flow edited The purpose of this page is to keep track of the articles that Lior is asked to review and wishes …
    The purpose of this page is to keep track of the articles that Lior is asked to review and wishes to pass on to group members to review, and how we'll login to the various journals, etc. --Saheli
    (view changes)
    10:36 am

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