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Documentation touchup #75

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202483e
Documentation touchup
yihchii Aug 16, 2019
3599d23
Update README.md
yihchii Aug 21, 2019
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28 changes: 14 additions & 14 deletions README.md
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Expand Up @@ -108,9 +108,9 @@ This app will output a number of files, representing the outputs of each of the

Parliament2 is available as an app on DNAnexus at https://platform.dnanexus.com/app/parliament2 (note: a DNAnexus account is required to access this link; you can create one at https://platform.dnanexus.com/login). The documentation for the app is included both on the DNAnexus platform and in the `dx_app_code` directory of this repository. A DNAnexus account is required to access the platform.

To run Parliament2 on DNAnexus, your input BAM file must be already on the DNAnexus platform. To run Parliament2 using the graphic interface, simply click the "Run" button from the app page and select your inputs. To run Parliament2 using the command-line interface, run the command `dx run parliament2 -h` and follow the guide generated. For more information on running executables on DNAnexus, see the [guide to running apps and applets](https://wiki.dnanexus.com/Command-Line-Client/Running-Apps-and-Applets).
To run Parliament2 on DNAnexus, your input BAM file must be already on the DNAnexus platform. To run Parliament2 using the graphic interface, simply click the "Run" button from the app page and select your inputs. To run Parliament2 using the command-line interface, run the command `dx run parliament2 -h` and follow the guide generated. For more information on running executables on DNAnexus, see the [guide to running apps and applets](https://documentation.dnanexus.com/user/running-apps-and-workflows/running-apps-and-applets).
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General information on using DNAnexus can be found in the [official documentation](https://wiki.dnanexus.com/Home).
General information on using DNAnexus can be found in the [official documentation](https://documentation.dnanexus.com).

### Building Parliament2 on DNAnexus

Expand All @@ -122,10 +122,10 @@ To build Parliament2 on your own on DNAnexus, you will have to have built the Do

For more information about using DNAnexus, see the following links:

* [Tutorial for using Docker images on DNAnexus](https://wiki.dnanexus.com/Developer-Tutorials/Using-Docker-Images)
* [Tutorial for building apps on DNAnexus](https://wiki.dnanexus.com/Developer-Tutorials/Intro-to-Building-Apps)
* [Tutorial for using Docker images on DNAnexus](https://documentation.dnanexus.com/developer/apps/dependency-management/using-docker-images)
* [Tutorial for building apps on DNAnexus](https://documentation.dnanexus.com/developer/apps/intro-to-building-apps)

General information on using DNAnexus can be found in the [official documentation](https://wiki.dnanexus.com/Home).
General information on using DNAnexus can be found in the [official documentation](https://documentation.dnanexus.com).

#### Modifying Parliament2 on DNAnexus

Expand Down Expand Up @@ -169,17 +169,17 @@ The svviz tool can at times consume a large amount of memory, causing the applic
### Tool versions

#### Structural variant callers
* Breakdancer: [v1.4.3](https://github.com/genome/breakdancer/releases/tag/v1.4.3)
* BreakSeq2: [v2.2](http://bioinform.github.io/breakseq2/)
* CNVnator: [v0.3.3](https://github.com/abyzovlab/CNVnator/commit/de012f2bccfd4e11e84cf685b19fc138115f2d0d)
* Delly: [v0.7.2](https://github.com/dellytools/delly/releases/tag/v0.7.2)
* Lumpy: [v0.2.13](https://github.com/arq5x/lumpy-sv/commit/f466f61e02680796192b055e4c084fbb23dcc692)
* Manta: [v1.4.0](https://anaconda.org/bioconda/manta)
* Breakdancer: [v1.4.3](https://github.com/genome/breakdancer/tree/v1.4.3)
* BreakSeq2: [v2.2](https://github.com/bioinform/breakseq2/tree/2.2)
* CNVnator: [v0.3.3](https://github.com/abyzovlab/CNVnator/tree/v0.3.3)
* Delly: [v0.7.2](https://github.com/dellytools/delly/tree/v0.7.2)
* Lumpy: [v0.2.13](https://github.com/arq5x/lumpy-sv/tree/0.2.13)
* Manta: [v1.4.0](https://github.com/Illumina/manta/tree/v1.4.0)

#### Other tools
* SVTyper: [v0.7.0](https://github.com/hall-lab/svtyper/commit/5fc30763fd3025793ee712a563de800c010f6bea)
* svviz: [v1.5.2](https://github.com/svviz/svviz/commit/84acefa13bf0d4ad6e7e0f1d058aed6f16681142)
* SURVIVOR: [v1.0.3](https://github.com/fritzsedlazeck/SURVIVOR/commit/7c7731d71fa1cba017f470895fb3ef55f2812067)
* SVTyper: [v0.7.0](https://github.com/hall-lab/svtyper/tree/v0.7.0)
* svviz: [v1.5.2](https://github.com/svviz/svviz/tree/1.5.2)
* SURVIVOR: [v1.0.3](https://github.com/fritzsedlazeck/SURVIVOR/tree/1.0.3)

### Additional notes

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99 changes: 94 additions & 5 deletions dx_app_code/parliament2/dxapp.json
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"WGS"
],
"dxapi": "1.0.0",
"version": "0.1.11",
"version": "0.1.11a",
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I don't think 0.1.11a follows the semver spec. Is the a meant to be a pre-release modifier?

"inputSpec": [
{
"name": "illumina_bam",
Expand Down Expand Up @@ -263,15 +263,104 @@
]
},
"details": {
"upstreamUrl": "https://www.dnanexus.com/papers/Parliament_Info_Sheet.pdf",
"upstreamProjects":[
{
"name": "parliament2",
"repoUrl": "https://github.com/dnanexus/parliament2",
"version": "0.1.11",
"license": "Apache-2.0",
"licenseUrl": "https://github.com/dnanexus/parliament2/blob/b492db6d740f90593fac061d3301d65fe19dce61/LICENSE",
"author": "Samantha Zarate"
},
{
"name": "BreakDancer",
"repoUrl": "https://github.com/genome/breakdancer",
"version": "v1.4.3",
"license": "MIT",
"licenseUrl": "https://github.com/genome/breakdancer/blob/master/build-common/LICENSE.txt",
"author": "Ken Chen and Xian Fan"
},
{
"name": "BreakSeq2",
"repoUrl": "https://github.com/bioinform/breakseq2/tree/master",
"version": "v2.2",
"license": "BSD-2-Clause",
"licenseUrl": "https://github.com/bioinform/breakseq2/blob/cea3f8eca9a553ee31a1501081567dd0d594f92e/LICENSE.txt",
"author": "Alexej Abyzov"
},
{
"name": "CNVnator",
"repoUrl": "https://github.com/abyzovlab/CNVnator",
"version": "v0.3.3",
"license": "MIT",
"licenseUrl": "https://github.com/abyzovlab/CNVnator/blob/078684552f61984ff495bc63aa721dd90d0ce32f/license.rtf",
"author": "Alexej Abyzov"
},
{
"name": "Delly2",
"repoUrl": "https://github.com/dellytools/delly",
"version": "v0.7.2",
"license": "GPL-3.0-or-later",
"licenseUrl": "https://github.com/dellytools/delly/blob/08063fd5df5eb1266d6ab31decd9f6ab4861b03d/LICENSE",
"author": "Tobias Rausch"
},
{
"name": "LUMPY",
"repoUrl": "https://github.com/arq5x/lumpy-sv",
"version": "v0.2.13",
"license": "MIT",
"licenseUrl": "https://github.com/arq5x/lumpy-sv/blob/f194e6f7bc6722b0118d80a73cd27462fd6204d6/LICENSE",
"author": "Ryan M Layer, Colby Chiang, Aaron R Quinlan, and Ira M Hall"
},
{
"name": "manta",
"repoUrl": "https://github.com/Illumina/manta",
"version": "v1.4.0",
"license": "GPL-3.0-or-later",
"licenseUrl": "https://github.com/Illumina/manta/blob/a7eaafedd8bb67589b8ab3efa65fdc2c1caa7e79/LICENSE.txt",
"author": "Xiaoyu Chen"
},
{
"name": "SVTyper",
"repoUrl": "https://github.com/hall-lab/svtyper",
"version": "v0.7.0",
"license": "MIT",
"licenseUrl": "https://github.com/hall-lab/svtyper/blob/5a1bb364e2ec7bb1a6ce16a9ca3d8c5d86ba0da7/LICENSE",
"author": "Colby Chiang"
},
{
"name": "svviz",
"repoUrl": "https://github.com/svviz/svviz",
"version": "1.5.2",
"license": "MIT",
"licenseUrl": "https://github.com/svviz/svviz/blob/53efd73598ce2cba151b5c64487d58647058483a/LICENSE",
"author": "Colby Chiang"
},
{
"name": "SURVIVOR",
"repoUrl": "https://github.com/svviz/svviz",
"version": "v1.0.3",
"license": "MIT",
"licenseUrl": "https://github.com/fritzsedlazeck/SURVIVOR/blob/542f9a1b61bd0f46f3ca49779e543af67b44cd14/LICENSE",
"author": "Daniel C. Jeffares and Fritz J. Sedlazeck"
}
],
"contactOrgs": [
"org-dnanexus"
],
"citations": [
"doi:10.1186/s12864-015-1479-3"
"doi:10.1101/424267",
"doi:10.1038/nmeth.1363",
"doi:10.1038/ncomms8256",
"doi:10.1101/gr.114876.110",
"doi:10.1093/bioinformatics/bts378",
"doi:10.1186/gb-2014-15-6-r84",
"doi:10.1093/bioinformatics/btv710",
"doi:10.1038/nmeth.3505",
"doi:bioinformatics/btv478",
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Doesn't resolve on https://www.doi.org/. Just double-check in the UI

"doi:10.1038/ncomms14061"
],
"upstreamAuthor": "Baylor College of Medicine",
"whatsNew": "* 0.1.11: Resolved OOM bug breaking svviz.\n* 0.1.10: Resolved bug breaking SVTyper; added Singularity functionality; modify run on DNAnexus.\n* 0.1.9: Add more logging functionality; resolved bug breaking SVVIZ; improved documentation; migrate to all regions; more sophisticated BAM storage management; other bug fixes.\n* 0.1.8: Add optional upload of log files; update SURVIVOR; add quality scores; improved error messaging; bug fixes.\n* 0.1.7: Update CNVnator, SVTyper; bug fixes.\n* 0.1.6: Bug fixes.\n* 0.1.5: Dockerized Parliament2.\n* 0.1.0: Adding Parliament2."
"whatsNew": "* 0.1.11a: Upstream software documentation update.\n* 0.1.11: Resolved OOM bug breaking svviz.\n* 0.1.10: Resolved bug breaking SVTyper; added Singularity functionality; modify run on DNAnexus.\n* 0.1.9: Add more logging functionality; resolved bug breaking SVVIZ; improved documentation; migrate to all regions; more sophisticated BAM storage management; other bug fixes.\n* 0.1.8: Add optional upload of log files; update SURVIVOR; add quality scores; improved error messaging; bug fixes.\n* 0.1.7: Update CNVnator, SVTyper; bug fixes.\n* 0.1.6: Bug fixes.\n* 0.1.5: Dockerized Parliament2.\n* 0.1.0: Adding Parliament2."
},
"regionalOptions": {
"aws:us-east-1": {
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