Commit 5f00e198 authored by bow's avatar bow
Browse files

Update Gentrap docs with examples

parent a24c96ad
{
"samples" : {
"sampleA" : {
"libraries" : {
"lib_1" : {
"R1" : "/path/to/inputA_R1.fq.gz",
"R2" : "/path/to/inputA_R2.fq.gz"
}
}
},
"sampleB" : {
"libraries" : {
"lib_1" : {
"R1" : "/path/to/inputB_1_R1.fq.gz",
"R2" : "/path/to/inputB_1_R2.fq.gz"
},
"lib_2": {
"R1" : "/path/to/inputB_2_R1.fq.gz",
"R2" : "/path/to/inputB_2_R2.fq.gz"
}
}
}
},
"gentrap": {
"output_dir": "/path/to/output_dir",
"expression_measures": ["fragments_per_gene", "bases_per_gene", "bases_per_exon"],
"strand_protocol": "non_specific",
"aligner": "gsnap",
"reference": "/share/isilon/system/local/Genomes-new-27-10-2011/H.Sapiens/hg19_nohap/gsnap/reference.fa",
"annotation_gtf": "/path/to/data/annotation/ucsc_refseq.gtf",
"annotation_bed": "/path/to/data/annotation/ucsc_refseq.bed",
"annotation_refflat": "/path/to/data/annotation/ucsc_refseq.refFlat",
"gsnap": {
"dir": "/share/isilon/system/local/Genomes-new-27-10-2011/H.Sapiens/hg19_nohap/gsnap",
"db": "hg19_nohap",
"quiet_if_excessive": true,
"npaths": 1
},
"cutadapt": {
"minimum_length": 20
},
"mapping": {
"flexiprep": {
"fastqc": {
"threads": 6,
"nogroup": true
}
}
},
"rawbasecounter": {
"vmem": "20G"
}
}
}
......@@ -110,18 +110,23 @@ Thus, an example settings configuration is as follows:
}
~~~
#### Example configurations
In most cases, it's practical to combine the samples and settings configuration into one file. Here is an [example config file](/examples/gentrap_example.json) where both samples and settings are stored into one file. Note also that there are additional tool configurations in the config file.
## Running Gentrap
As with other pipelines in the Biopet suite, Gentrap can be run by specifying the pipeline after the `pipeline` subcommand:
~~~
java -jar </path/to/biopet.jar> pipeline gentrap -config </path/to/config.json> -qsub -jobParaEnv BWA -run
$ java -jar </path/to/biopet.jar> pipeline gentrap -config </path/to/config.json> -qsub -jobParaEnv BWA -run
~~~
If you already have the `biopet` environment module loaded, you can also simply call `biopet`:
You can also use the `biopet` environment module (recommended) when you are running the pipeline in SHARK:
~~~
biopet pipeline gentrap -config </path/to/config.json> -qsub -jobParaEnv BWA -run
$ module load biopet/v0.3.1
$ biopet pipeline gentrap -config </path/to/config.json> -qsub -jobParaEnv BWA -run
~~~
It is also a good idea to specify retries (we recomend `-retry 3` up to `-retry 5`) so that cluster glitches do not interfere with your pipeline runs.
......
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