Commit bbc08fd5 authored by Wai Yi Leung's avatar Wai Yi Leung
Browse files

unify biopet invocation command from java -jar <biopet.jar> to `biopet`

parent 568b6579
......@@ -48,6 +48,24 @@ $ biopet pipeline <pipeline_name> -config <path/to/config.json> -qsub -jobParaEn
It is usually a good idea to do the real run using `screen` or `nohup` to prevent the job from terminating when you log out of SHARK. In practice, using `biopet` as it is is also fine. What you need to keep in mind, is that each pipeline has their own expected config layout. You can check out more about the general structure of our config files [here](general/config.md). For the specific structure that each pipeline accepts, please consult the respective pipeline page.
### Convention in this documentation
To unify the commands used in the examples, we agree on the following:
Whenever an example command starts with `biopet` as in:
```
biopet tool ...
```
One can replace the `biopet` command with:
```
java -jar </path/to/biopet.jar> tool
```
The `biopet` shortcut is only available on the SHARK cluster with the `module` environment installed.
### Running Biopet in your own computer
At the moment, we do not provide links to download the Biopet package. If you are interested in trying out Biopet locally, please contact us as [sasc@lumc.nl](mailto:sasc@lumc.nl).
......
......@@ -67,14 +67,14 @@ Specific configuration options additional to Basty are:
##### For the help screen:
~~~
java -jar </path/to/biopet.jar> pipeline basty -h
biopet pipeline basty -h
~~~
##### Run the pipeline:
Note that one should first create the appropriate [configs](../general/config.md).
~~~
java -jar </path/to/biopet/jar> pipeline basty -run -config MySamples.json -config MySettings.json
biopet pipeline basty -run -config MySamples.json -config MySettings.json
~~~
### Result files
......
......@@ -59,7 +59,7 @@ While optional settings are:
As with other pipelines in the Biopet suite, Carp can be run by specifying the pipeline after the `pipeline` subcommand:
~~~ bash
java -jar </path/to/biopet.jar> pipeline carp -config </path/to/config.json> -qsub -jobParaEnv BWA -run
biopet pipeline carp -config </path/to/config.json> -qsub -jobParaEnv BWA -run
~~~
If you already have the `biopet` environment module loaded, you can also simply call `biopet`:
......
......@@ -13,7 +13,7 @@ Flexiprep only works on `.fastq` files.
To get the help menu:
``` bash
java -jar </path/to/biopet.jar> pipeline Flexiprep -h
biopet pipeline Flexiprep -h
Arguments for Flexiprep:
-R1,--input_r1 <input_r1> R1 fastq file (gzipped allowed)
......
......@@ -16,7 +16,7 @@ Pipeline analysis components include:
To get the help menu:
``` bash
java -jar </path/to/biopet.jar> pipeline Gears -h
biopet pipeline Gears -h
... default config ...
......@@ -40,7 +40,7 @@ Note that the pipeline also works on unpaired reads where one should only provid
To start the pipeline (remove `-run` for a dry run):
``` bash
java -jar Biopet-0.5.0.jar pipeline Gears -run \
biopet pipeline Gears -run \
-R1 myFirstReadPair -R2 mySecondReadPair -sample mySampleName \
-library myLibname -config mySettings.json
```
......
......@@ -119,7 +119,7 @@ In most cases, it's practical to combine the samples and settings configuration
As with other pipelines in the Biopet suite, Gentrap can be run by specifying the pipeline after the `pipeline` subcommand:
~~~ bash
$ java -jar </path/to/biopet.jar> pipeline gentrap -config </path/to/config.json> -qsub -jobParaEnv BWA -run
biopet pipeline gentrap -config </path/to/config.json> -qsub -jobParaEnv BWA -run
~~~
You can also use the `biopet` environment module (recommended) when you are running the pipeline in SHARK:
......
......@@ -91,7 +91,7 @@ Any supplied sample config will be ignored.
For the help menu:
~~~
java -jar </path/to/biopet.jar> pipeline mapping -h
biopet pipeline mapping -h
Arguments for Mapping:
-R1,--input_r1 <input_r1> R1 fastq file
......@@ -107,7 +107,7 @@ Arguments for Mapping:
To run the pipeline:
~~~
java -jar </path/to/biopet.jar> pipeline mapping -run --config mySettings.json \
biopet pipeline mapping -run --config mySettings.json \
-R1 myReads1.fastq -R2 myReads2.fastq
~~~
Note that removing -R2 causes the pipeline to assume single end `.fastq` files.
......
......@@ -35,7 +35,7 @@ Specific configuration values for the Sage pipeline are:
As with other pipelines, you can run the Sage pipeline by invoking the `pipeline` subcommand. There is also a general help available which can be invoked using the `-h` flag:
~~~
$ java -jar /path/to/biopet.jar pipeline sage -h
$ biopet pipeline sage -h
Arguments for Sage:
-s,--sample <sample> Only Sample
......@@ -56,7 +56,7 @@ $ biopet pipeline sage
To run the pipeline:
~~~
biopet pipeline sage -config /path/to/config.json -qsub -jobParaEnv BWA -run
$ biopet pipeline sage -config /path/to/config.json -qsub -jobParaEnv BWA -run
~~~
......
......@@ -30,7 +30,7 @@ The full pipeline can start from fastq or from bam file. This pipeline will incl
To view the help menu, execute:
~~~
java -jar </path/to/biopet.jar> pipeline shiva -h
biopet pipeline shiva -h
Arguments for Shiva:
-sample,--onlysample <onlysample> Only Sample
......@@ -41,7 +41,7 @@ Arguments for Shiva:
To run the pipeline:
~~~
java -jar </path/to/biopet.jar> pipeline shiva -config MySamples.json -config MySettings.json -run
biopet pipeline shiva -config MySamples.json -config MySettings.json -run
~~~
A dry run can be performed by simply removing the `-run` flag from the command line call.
......@@ -67,7 +67,7 @@ Arguments for ShivaVariantcalling:
To run the pipeline:
~~~
java -jar </path/to/biopet.jar> pipeline shivavariantcalling -config MySettings.json -run
biopet pipeline shivavariantcalling -config MySettings.json -run
~~~
A dry run can be performed by simply removing the `-run` flag from the command line call.
......
......@@ -58,13 +58,13 @@ Running the pipeline
The command to run the pipeline is:
~~~~ bash
java -jar pipeline Toucan -Input <input_vcf> -config <config_json> -run
biopet pipeline Toucan -Input <input_vcf> -config <config_json> -run
~~~~
If one wishes to run it on a cluster, the command becomes:
~~~~ bash
java -jar pipeline Toucan -Input <input_vcf> -config <config_json> -run -qsub -jobParaEnv <PE>
biopet pipeline Toucan -Input <input_vcf> -config <config_json> -run -qsub -jobParaEnv <PE>
~~~~
......
......@@ -8,7 +8,7 @@ It can be very useful to produce the right input needed for follow up tools, for
To get the help menu:
~~~bash
java -jar Biopet-0.2.0-DEV-801b72ed.jar tool BastyGenerateFasta -h
biopet tool BastyGenerateFasta -h
Usage: BastyGenerateFasta [options]
......
......@@ -8,7 +8,7 @@ It captures for example the # of mapped reads, # of duplicates, # of mates unmap
## Example
To get the help menu:
~~~
java -jar Biopet-0.2.0.jar tool BiopetFlagstat -h
biopet tool BiopetFlagstat -h
Usage: BiopetFlagstat [options]
-l <value> | --log_level <value>
......@@ -25,7 +25,7 @@ Usage: BiopetFlagstat [options]
To run the tool:
~~~
java -jar Biopet-0.2.0.jar tool BiopetFlagstat -I myBAM.bam
biopet tool BiopetFlagstat -I myBAM.bam
~~~
### Output
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......@@ -6,7 +6,7 @@ This tool has been written to check the allele frequency in BAM files.
## Example
To get the help menu:
~~~
java -jar Biopet-0.2.0.jar tool CheckAllelesVcfInBam -h
biopet tool CheckAllelesVcfInBam -h
Usage: CheckAllelesVcfInBam [options]
-l <value> | --log_level <value>
......@@ -28,7 +28,7 @@ Usage: CheckAllelesVcfInBam [options]
To run the tool:
~~~
java -jar Biopet-0.2.0.jar tool CheckAllelesVcfInBam --inputFile myVCF.vcf \
biopet tool CheckAllelesVcfInBam --inputFile myVCF.vcf \
--bam myBam1.bam --sample bam_sample1 --outputFile myAlleles.vcf
~~~
......@@ -37,7 +37,7 @@ The only thing one needs to make sure off is matching the `--bam` and `--sample`
For multiple bam files:
~~~
java -jar Biopet-0.2.0.jar tool CheckAllelesVcfInBam --inputFile myVCF.vcf \
biopet tool CheckAllelesVcfInBam --inputFile myVCF.vcf \
--bam myBam1.bam --sample bam_sample1 --bam myBam2.bam --sample bam_sample2 \
--bam myBam3.bam --sample bam_sample3 --outputFile myAlleles.vcf
~~~
......
......@@ -9,7 +9,7 @@ The tool is also very usefull to create test data sets.
## Example
To get the help menu:
~~~
java -jar Biopet-0.2.0.jar tool ExtractAlignedFastq -h
biopet tool ExtractAlignedFastq -h
ExtractAlignedFastq - Select aligned FASTQ records
Usage: ExtractAlignedFastq [options]
......@@ -42,7 +42,7 @@ This tool creates FASTQ file(s) containing reads mapped to the given alignment i
To run the tool:
~~~
java -jar Biopet-0.2.0.jar tool ExtractAlignedFastq \
biopet tool ExtractAlignedFastq \
--input_file myBam.bam --in1 myFastq_R1.fastq --out1 myOutFastq_R1.fastq --interval myTarget.bed
~~~
* Note that this tool works for single end and paired end data. The above example can be easily extended for paired end data.
......
......@@ -9,7 +9,7 @@ needed for the number of chunks specified. Note that this will be automatically
## Example
To get the help menu:
~~~
java -jar Biopet-0.2.0.jar tool FastqSplitter -h
biopet tool FastqSplitter -h
Usage: FastqSplitter [options]
-l <value> | --log_level <value>
......@@ -25,7 +25,7 @@ Usage: FastqSplitter [options]
~~~
To run the tool:
~~~
java -jar Biopet-0.2.0.jar tool FastqSplitter --inputFile myFastq.fastq \
biopet tool FastqSplitter --inputFile myFastq.fastq \
--output mySplittedFastq_1.fastq --output mySplittedFastq_2.fastq \
--output mySplittedFastq_3.fastq
~~~
......
......@@ -9,7 +9,7 @@ those regions with the BAM file. On those extracted regions the tool will perfor
## Example
To get the help menu:
~~~
java -jar Biopet-0.2.0.jar tool FindRepeatsPacBio -h
biopet tool FindRepeatsPacBio -h
Usage: FindRepeatsPacBio [options]
-l <value> | --log_level <value>
......@@ -26,7 +26,7 @@ Usage: FindRepeatsPacBio [options]
To run the tool:
~~~
java -jar Biopet-0.2.0.jar tool FindRepeatsPacBio --inputBam myInputbam.bam \
biopet tool FindRepeatsPacBio --inputBam myInputbam.bam \
--inputBed myRepeatRegions.bed > mySummary.txt
~~~
Since the default output of the program is printed in stdout we can use > to write the output to a text file.
......
......@@ -7,7 +7,7 @@ This tool is used to merge overlapping alleles.
## Example
To get the help menu:
~~~
java -jar Biopet-0.2.0.jar tool MergeAlleles -h
biopet tool MergeAlleles -h
Usage: MergeAlleles [options]
-l <value> | --log_level <value>
......
......@@ -11,13 +11,13 @@ so usually one does not want to safe these files.
## Example
To start the tool:
~~~ bash
java -jar Biopet-0.2.0.jar tool mpileupToVcf
biopet tool mpileupToVcf
~~~
To open the help:
~~~ bash
java -jar Biopet-0.2.0.jar tool mpileupToVcf -h
biopet tool mpileupToVcf -h
Usage: MpileupToVcf [options]
-l <value> | --log_level <value>
......
......@@ -4,13 +4,13 @@ This tool enables a user to create a full sample sheet in JSON format suitable f
The tool can be started as follows:
~~~ bash
java -jar <Biopet.jar> tool SamplesTsvToJson
biopet tool SamplesTsvToJson
~~~
To open the help:
~~~ bash
java -jar Biopet-0.2.0.jar tool SamplesTsvToJson -h
biopet tool SamplesTsvToJson -h
Usage: SamplesTsvToJson [options]
-l <value> | --log_level <value>
......
......@@ -9,7 +9,7 @@ There is a wide set of options which one can use to change the filter settings.
To open the help menu:
~~~ bash
java -jar Biopet-0.2.0.jar tool VcfFilter -h
boppet tool VcfFilter -h
Usage: VcfFilter [options]
-l <value> | --log_level <value>
......@@ -49,7 +49,7 @@ Usage: VcfFilter [options]
To run the tool:
~~~ bash
java -jar Biopet-0.2.0.jar tool VcfFilter --inputVcf myInput.vcf \
biopet tool VcfFilter --inputVcf myInput.vcf \
--outputVcf myOutput.vcf --filterRefCalls --minSampleDepth
~~~
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