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updated readme

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1 parent 38eefe5 commit 5bed8d9e34096c3ea3176f36cfa46f2ead178aba @fstrozzi committed Sep 24, 2012
Showing with 4 additions and 4 deletions.
  1. +4 −4 README.md
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@@ -82,13 +82,13 @@ For a complete list of current BioGrid parameters, type "bio-grid -h":
-s, --split-number NUMBER Number of input files (or group of files) to use per job. If all the files in a location need to be used for a single job, just specify 'all'
-p, --processes PROCESSES Number of processes per job
-c, --command-line COMMANDLINE Command line to be executed
- -o, --output OUTPUT Output folder
+ -o, --output OUTPUT Output folder. Needs a <output> placeholder in the command line
-r, --copy-to LOCATION Copy the output once a job is terminated
-e, --erease-output Delete job output data when completed (useful to delete output temporary files on a computing node)
- -a, --params PARAM1,PARAM2... List of parameters to use for sampling
+ -a, --params PARAM1,PARAM2... List of parameters to use for testing. Needs a <param> placeholder in the command line
-d, --dry Dry run. Just write the job scripts without sending them in queue (for debugging or testing)
-t, --test Start the mapping only with the first group of reads (e.g. for testing parameters)
- -i, --input INPUT1,INPUT2... Location where to find input files (accepts wildcards). You can specify more than one input location, just provide a comma separated list
+ -i, --input INPUT1,INPUT2... Location where to find input files (accepts wildcards). Needs <input(1,2,3...> placeholder(s) in the command line
--sep SEPARATOR Input file separator [Default: , ]
--keep-scripts Keep all the running scripts created for all the jobs
-h, --help Display this screen
@@ -129,7 +129,7 @@ If you want to sample non-numerical parameters, with BioGrid it is possible to u
bio-grid -i "/data/Project_X/Sample_Y/*_R1_*.fastq.gz","/data/Project_X/Sample_Y/*_R2_*.fastq.gz" -n bowtie_mapping -c "/software/bowtie2 -x /genomes/genome_index -p 8 <param> -1 <input1> -2 <input2> > <output>.sam" -o /data/Project_X/Sample_Y_mapping -s 1 -p 8 -r /results/Sample_Y_mapping -e --param "--sensitive","--very-sensitive","--fast" -t
```
-In this case, the key points are the ```<param>``` placeholder in the command line and the corresponding ```--params``` options in BioGrid, which specify a list of parameters to be used to generate and run different jobs, each one with a different parameter in the list. Again, even in this case, it is recommended to do parameters testing using the ```-t``` options, which only run a single job and not the full job array.
+In this case, the key points are the ```<param>``` placeholder in the command line and the corresponding ```--params``` options in BioGrid, which specify a list of parameters to be used to generate and run different jobs, each one with a different parameter in the list. Again, even in this case, it is recommended to do parameters testing using the ```-t``` option, which only runs a single job and not the full job array.
So far, BioGrid does not support, for each run, sampling more than one parameter at the same time.

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