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https://github.com/pwwang/conda-jvarkit
Recipts for building jvarkit tools on conda
https://github.com/pwwang/conda-jvarkit
Last synced: 14 days ago
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Recipts for building jvarkit tools on conda
- Host: GitHub
- URL: https://github.com/pwwang/conda-jvarkit
- Owner: pwwang
- License: gpl-3.0
- Created: 2019-08-23T17:49:39.000Z (over 5 years ago)
- Default Branch: master
- Last Pushed: 2020-06-06T00:31:58.000Z (over 4 years ago)
- Last Synced: 2024-12-10T04:27:13.351Z (24 days ago)
- Language: Python
- Homepage:
- Size: 26.4 KB
- Stars: 1
- Watchers: 3
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# conda-jvarkit
Receipts for building jvarkit tools on conda
## Build jvarkit for conda
```shell
> python build.py build
```
## Run jvarkit
```shell
> jvarkit
Usage:
jvarkit [OPTIONS]
Available commands:
install - Install a jvarkit tool.
list - List available jvarkit tools.
version - Show current version of jvarkit.
help [COMMAND] - Print help message for the command and exit.
Installed tools:
vcfstats - Produce VCF statitics
vcf2bam - vcf to bam
vcfgo - Find the GO terms for VCF annotated with SNPEFF or VEP
```
## Run a single tool
```shell
> jvarkit vcfgo
There was an error in the input parameters.
The following options are required: [-G], [-A]
[INFO][Launcher]vcfgo Exited with failure (-1)
Description:
Find the GO terms for VCF annotated with SNPEFF or VEP
Usage:
jvarkit vcfgo [OPTIONS]
Optional options:
--hh [BOOL] - Show original help page.
Default: False
--java - Path to java executable.
Default: 'java'
-h, -H, --help - Show help message and exit.
Java options:
-X../-D.. - Java Virtual Machine Parameters
Required tool options:
-A - (goa input url)
Default: http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/gene- \
associations/gene_association.goa_human.gz?rev=HEAD
-G - (go url)
Default: http://archive.geneontology.org/latest-termdb/go_daily- \
termdb.rdf-xml.gz
Optional tool options:
-h, --help - print help and exit
--helpFormat - What kind of help. One of [usage,markdown,xml].
-o, --output - Output file. Optional . Default: stdout
--version - print version and exit
-C - (Go:Term) Add children to the list of go term to be filtered. Can be
used multiple times.
Default: []
-F - if -C is used, don't remove the variant but set the filter
-T - INFO tag.
Default: GOA
-r - remove variant if no GO term is found associated to variant
Default: false
-v - inverse filter if -C is used
Default: false
```