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              grep rough audit - static analysis tool
                  v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
bcbio-1.2.4/config/examples/NA12878.validate.sh-29-do
bcbio-1.2.4/config/examples/NA12878.validate.sh:30:    echo snp $f `bcftools view --types snps rtg/$f.vcf.gz | grep -vc "^#"` >> $1.stat
bcbio-1.2.4/config/examples/NA12878.validate.sh:31:    echo indels $f `bcftools view --exclude-types snps rtg/$f.vcf.gz | grep -vc "^#"` >> $1.stat
bcbio-1.2.4/config/examples/NA12878.validate.sh-32-done
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bcbio-1.2.4/docs/contents/cwl.md-56-```
bcbio-1.2.4/docs/contents/cwl.md:57:In the above commands, the _bcbio-vm_ install goes in `$TARGETDIR`. The example is in your home directory but set it anywhere you have space. Also, as an alternative to symbolic linking to a `$BINDIR`, you can add the install bin directory to your PATH:
bcbio-1.2.4/docs/contents/cwl.md-58-```shell
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bcbio-1.2.4/docs/contents/cwl.md-205-Set some useful environmental variables:
bcbio-1.2.4/docs/contents/cwl.md:206:* `$PNAME` -- The name of the project you're analyzing. For convenience here we keep this the same for your local files and remote DNAnexus project, although that does not have to be true.
bcbio-1.2.4/docs/contents/cwl.md:207:* `$DX_AUTH_TOKEN` -- The DNAnexus authorization token for access, used for the `dx` command line tool and bcbio scripts.
bcbio-1.2.4/docs/contents/cwl.md:208:* `$DX_PROJECT_ID` -- The DNAnexus GUID identifier for your project (similar to `project-F8Q7fJj0XFJJ3XbBPQYXP4B9`). You can get this from `dx env` after creating/selecting a project in steps 1 and 2.
bcbio-1.2.4/docs/contents/cwl.md-209-
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bcbio-1.2.4/docs/contents/cwl.md-306-
bcbio-1.2.4/docs/contents/cwl.md:307:1. Since Seven Bridges is available on multiple platforms and data access points, we authenticate with a configuration file in `$HOME/.sevenbridges/credentials` with potentially [multiple profiles defining API access URLs and authentication keys](https://sevenbridges-python.readthedocs.io/en/latest/quickstart/#initialize-the-library-using-a-configuration-file). We reference the [specified credentials](https://docs.sevenbridges.com/docs/store-credentials-to-access-seven-bridges-client-applications-and-libraries#section-unified-configuration-file) when setting up a `bcbio_system-sbg.yaml` file to ensure correct authentication.
bcbio-1.2.4/docs/contents/cwl.md-308-
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bcbio-1.2.4/docs/contents/development.md-56-
bcbio-1.2.4/docs/contents/development.md:57:To install in `${HOME}/local/share/bcbio` (your location might be different, make sure you have ~30GB of disk quota there):
bcbio-1.2.4/docs/contents/development.md-58-```shell
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bcbio-1.2.4/docs/contents/development.md-74-Or directly call the testing bcbio:
bcbio-1.2.4/docs/contents/development.md:75:`${HOME}/local/share/bcbio/anaconda/bin/bcbio_nextgen.py`.
bcbio-1.2.4/docs/contents/development.md-76-
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bcbio-1.2.4/docs/contents/parallel.md-53-
bcbio-1.2.4/docs/contents/parallel.md:54:Specify an [SGE parallel environment](https://docs.oracle.com/cd/E19957-01/820-0698/6ncdvjcmd/index.html) that supports using multiple cores on a single node with `-r pename=your_pe`. Since this setup is system specific it is hard to write general code for find a suitable environment. Specifically, when there are multiple usable parallel environments, it will select the first one which may not be correct. Manually specifying it with a `pename=` flag to resources will ensure correct selection of the right environment. If you're administering a grid engine cluster and not sure how to set this up you'd typically want a `smp` queue using `allocation_rule: $pe_slots` like in this [example pename configuration](https://github.com/WGLab/biocluster/blob/431a05f6dfd532205aacfc7477ac740b0e7b2a0a/03%20System%20customization.md#setting-up-parallel-environment) or [smp template](https://gist.github.com/dan-blanchard/6586533#file-smp_template).
bcbio-1.2.4/docs/contents/parallel.md-55-
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bcbio-1.2.4/docs/contents/small_rnaseq.md-29-## Parameters
bcbio-1.2.4/docs/contents/small_rnaseq.md:30:* `adapters` The 3' end adapter that needs to be remove. For NextFlex protocol you can add `adapters: ["4N", "$3PRIME_ADAPTER"]`. For any other options you can use resources: `atropos:options:["-u 4", "-u -4"]`.
bcbio-1.2.4/docs/contents/small_rnaseq.md-31-* `species` 3 letters code to indicate the species in mirbase classification (i.e. hsa for human).