start:software:topical:lifesciences:ngs:local_search_tools

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start:software:topical:lifesciences:ngs:local_search_tools [2020/10/02 14:48]
jrutte02
start:software:topical:lifesciences:ngs:local_search_tools [2021/06/16 16:22] (current)
meesters
Line 40: Line 40:
  
 ''bio/lambda'' -- the application is ''lambda2'' ''bio/lambda'' -- the application is ''lambda2''
- 
-===== The Wrapper Module on MOGON ===== 
- 
-We provide a wrapper module on MOGON in order to aggregate jobs and the searches. 
- 
-The wrapper script is available as a [[:start:working_on_mogon:workflow_organization:setting_up_environment_modules|module]]: 
- 
-''bio/parallel_BLAST'' 
- 
-The code is under version management and hosted internally, [[https://gitlab.rlp.net/hpc-jgu-lifescience/seq-analysis|here]]. 
- 
-==== Limitations ==== 
- 
-<callout type="danger" icon="true"> 
-This wrapping module has - despite the fact, that is the oldest wrapper for life scientist on MOGON - serious shortcomings:  
-  * currently only support for BLAST+ applications 
-  * the output is not automatically merged to be conveniently analyzed in down-stream tools 
-  * reference databases are limited in their size: only those which fit in the RAM of a node can be analyzed. 
-  * the batch system abstraction reaches not as far as for the other modules, e.g. a user has to estimate the requested ramdisk size (see below) by herself 
-  * the wrapping module is currently only implemented for MOGON I.  
- 
-If you need a tool resp. wrapper to reach beyond these limitations, get in touch with us. 
-</callout> 
- 
-==== Usage ==== 
- 
-Calling ''LA_Wrapper -h'' will display a help message with all the options, the script provides. Likewise, the call ''LA_Wrapper --credits'' will display credits and a version history. 
- 
-<callout type="warning" icon="true"> 
-The wrapper script will submit a job, it is not intended to be just within a SLURM environment, but rather creates one. 
-</callout> 
- 
-The script, after loading the module, can then be run like: 
- 
-<code bash> 
-$ LA_Wrapper [options] <fastafile> <database> 
-</code> 
- 
-About Arguments: 
-  * ''fastafile'' needs to be a (relative) path to a file containing all inputs in FASTA format. 
- 
-The options: 
-  * ''LA_Wrapper'' attempts to deduce your SLURM account. This may fail, in which case ''-A, --account'' needs to be supplied. 
-  * ''-l,--runlimit'', this defaults to 300 minutes. 
-  *  
-  * ''--reservation'', reservation to use  (none is the default) 
-  * ''--time'', time in minutes  (300 is the default) 
-  * ''-r,--ramdisk'', ramdisk size in units of GiB (default is 40 GiB) 
-  * ''-t,--threads'', blast threads (default is 8) 
-  * ''--blastparams'', blast parameters (default is -outfmt 5 (for xml output)) 
-  * ''-s,--splitup'', No. of FASTA sequences per query file (default is 20) 
-  * ''--blastdir'', output directory (default is composition of input names) 
-  * ''--executable'', choose executable (currently only from NCBI-BLAST, default: blastx) 
-  * ''--compress'', if set, the output files will be merged and compressed (time consuming!, defaultt: off) 
-  * ''--test'', ''--no-test'', dry run, testing only (off by default) 
- 
-Output: 
-  * One analysis per input as specified by the respective executable. 
  
  • start/software/topical/lifesciences/ngs/local_search_tools.txt
  • Last modified: 2021/06/16 16:22
  • by meesters