Ignore:
Timestamp:
Aug 5, 2014, 2:39:32 PM (7 years ago)
Author:
Nicklas Nordborg
Message:

References #614: Improve error handling when executing jobs on the cluster

Re-organized the configuration file which should make it easier to re-use some configuration settings and also to understand when the different settings are used.

File:
1 edited

Legend:

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  • extensions/net.sf.basedb.reggie/trunk/reggie-ogs-hosts.xml

    r2553 r2555  
    1616    <!-- job-folder: must be a path that is common to the master and all nodes (required) -->
    1717    <job-folder>/path/to/job/folder</job-folder>
     18   
    1819    <!-- tmp-folder: can be a local path on the node but must exist on all nodes (required) -->
    1920    <tmp-folder>/tmp</tmp-folder>
    20     <!-- script-folder: folder where the pipeline scripts are located (required).
    21       Must be accessible from all nodes.
    22      -->
    23     <script-folder>/path/to/script/folder</script-folder>
     21   
     22    <!-- full path to the location where HiSeq data is stored (required) -->
     23    <run-archive>/path/to/run_archive</run-archive>
    2424   
    2525    <!-- Full path to the location where data files should be archived (required) -->
     
    3030    <!-- Do not include name of project -->
    3131    <reference-folder>/disk/reference</reference-folder>
     32   
     33    <!-- Information about programs used by reggie -->
     34    <!-- Unless otherwise noted, all paths must be the same on all nodes -->
     35    <programs>
     36      <pipeline-scripts>
     37        <!-- folder where the pipeline scripts are located (required). -->
     38        <path>/path/to/pipelinescripts</path>
     39      </pipeline-scripts>
     40      <picard>
     41        <!-- full path to the directory with Picard jar files (required) -->
     42        <path>/path/to/picard</path>
     43      </picard>
     44      <trimmomatic>
     45        <!-- full path to the JAR file with the Trimmomatic program (required) -->
     46        <path>/usr/local/packages/trimmomatic/0.32/trimmomatic-0.32.jar</path>
     47        <!-- full path to the file with Illumina adapter information -->
     48        <adapter-file>/usr/local/packages/trimmomatic/0.32/adapters/TruSeq3-PE-2.fa</adapter-file>
     49      </trimmomatic>
     50      <bowtie2>
     51        <!-- full or partial path to bowtie2 (required) -->
     52        <path>bowtie2</path>
     53      </bowtie2>
     54      <tophat>
     55        <!-- full or partial path to tophat (required) -->
     56        <path>tophat</path>
     57      </tophat>
     58    </programs>
    3259   
    3360    <!-- priority values that are selectable in the web interface -->
     
    4269    <!-- settings for the demuxing step -->
    4370    <demux>
    44       <!-- full path to the directory with Picard jar files (required) -->
    45       <picard-dir></picard-dir>
    46       <!-- amount of memory to give to Picard (default is 50g)-->
    47       <picard-memory>50g</picard-memory>
    4871      <!-- parallel environment option to the queue system -->
    4972      <!-- the default setting use all slots on hosts with at least 8 slots available -->
    5073      <parallel-environment>smp 8-</parallel-environment>
    51       <!-- full path to the location where HiSeq data is stored (required) -->
    52       <run-archive>/path/to/run_archive</run-archive>
     74      <!-- amount of memory to give to Picard (default is 50g)-->
     75      <picard-memory>50g</picard-memory>
    5376      <!-- static options for the picard ExtractIlluminaBarcodes step -->
    5477      <extract-options>QUIET=true VERBOSITY=WARNING</extract-options>
     
    5780      <!-- number of tiles to process when debugging (default=16) -->
    5881      <debug-tile-limit>16</debug-tile-limit>
     82      <!-- static options for Trimmomatic -->
     83      <trimmomatic-options>ILLUMINACLIP:${AdapterFile}:2:30:12:1:true LEADING:3 TRAILING:3 MAXINFO:40:0.9 MINLEN:20</trimmomatic-options>
    5984    </demux>
    6085
    61     <!-- Settings for the Trimmomatic step -->
    62     <trimmomatic>
    63       <!-- full path to the JAR file with the Trimmomatic program -->
    64       <jar-path>/usr/local/packages/trimmomatic/0.32/trimmomatic-0.32.jar</jar-path>
    65       <!-- full path to the file with Illumina adapter information -->
    66       <adapter-file>/usr/local/packages/trimmomatic/0.32/adapters/TruSeq3-PE-2.fa</adapter-file>
    67       <!-- static options for Trimmomatic -->
    68       <options>ILLUMINACLIP:${AdapterFile}:2:30:12:1:true LEADING:3 TRAILING:3 MAXINFO:40:0.9 MINLEN:20</options>
    69     </trimmomatic>
    70 
    71     <pe-filter>
    72       <!-- static options for bowtie -->
    73       <bowtie-options>-q --fr -k 1 --phred33 -t --local</bowtie-options>
    74 
     86    <mask>
    7587      <!-- parallel environment option to the queue system -->
    7688      <!-- the default setting use all slots on hosts with at least 8 slots available -->
    7789      <parallel-environment>smp 8-</parallel-environment>
    7890
    79       <!-- relative path from <reference-folder> to the reference genome used for filtering -->
    80       <!-- TODO selectable in GUI? saved as annotation? -->
     91      <!-- relative path from <reference-folder> to the reference genome used for masking -->
     92      <!-- This is the -x option used for bowtie -->
    8193      <reference-name>scanb/ribo_phix_repeats_filter.bt2/ribo_phix_repeats_filter</reference-name>
    82     </pe-filter>
     94     
     95      <!-- static options for bowtie -->
     96      <bowtie-options>-q --fr -k 1 --phred33 -t --local</bowtie-options>
     97    </mask>
    8398
    84     <tophat>
     99    <align>
    85100      <!-- relative path from <reference-folder> to the reference genome used for alignment -->
    86101      <!-- TODO selectable in GUI? saved as annotation? -->
    87102      <reference-gidx>scanb/hg19_1-22_XM_extra_b37_Y_decoy.bt2/hg19_1-22_XM_extra_b37_Y_decoy</reference-gidx>
    88103      <reference-tidx>scanb/UCSC_Human_hg19_knownGenes_GTF_appended_10sep2012v209.bt2/knownGenes</reference-tidx>
     104     
    89105      <!-- static options for tophat -->
    90       <options>--library-type fr-firststrand --keep-fasta-order --no-coverage-search</options>
    91     </tophat>
     106      <tophat-options>--library-type fr-firststrand --keep-fasta-order --no-coverage-search</tophat-options>
     107     
     108      <!-- static options for the picard MarkDuplicates step -->
     109      <mark-duplicates-options>REMOVE_DUPLICATES=false ASSUME_SORTED=true MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=2000 QUIET=true VERBOSITY=WARNING</mark-duplicates-options>
     110    </align>
    92111  </host>
    93112
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