From e1aa7824ba5aeb1c94da42e1bbe9fa681388f104 Mon Sep 17 00:00:00 2001 From: chapmanb Date: Wed, 16 Sep 2015 05:28:36 -0400 Subject: [PATCH] Update documentation links to bcb.io --- README.rst | 4 ++-- TODO.md | 2 +- docs/contents/installation.rst | 2 +- docs/contents/parallel.rst | 2 +- docs/contents/presentations.rst | 6 +++--- docs/contents/testing.rst | 4 ++-- 6 files changed, 10 insertions(+), 10 deletions(-) diff --git a/README.rst b/README.rst index 54b5bac99..f646beb56 100644 --- a/README.rst +++ b/README.rst @@ -43,8 +43,8 @@ Features .. _users page: https://bcbio-nextgen.readthedocs.org/en/latest/contents/introduction.html#users .. _developer documentation: https://bcbio-nextgen.readthedocs.org/en/latest/contents/code.html .. _variant calling and RNA-seq pipelines: https://bcbio-nextgen.readthedocs.org/en/latest/contents/pipelines.html -.. _parallel analysis and scaling: http://bcbio.wordpress.com/2013/05/22/scaling-variant-detection-pipelines-for-whole-genome-sequencing-analysis/ -.. _Automated validation: http://bcbio.wordpress.com/2014/05/12/wgs-trio-variant-evaluation/ +.. _parallel analysis and scaling: http://bcb.io/2013/05/22/scaling-variant-detection-pipelines-for-whole-genome-sequencing-analysis/ +.. _Automated validation: http://bcb.io/2014/05/12/wgs-trio-variant-evaluation/ Quick start ----------- diff --git a/TODO.md b/TODO.md index acece8ed1..577e0933e 100644 --- a/TODO.md +++ b/TODO.md @@ -64,7 +64,7 @@ These are roughly ordered by current priority and we welcome contributors. speed ups and parallelization. Integrate development work on [bcbio.variation.recall] using recalling with local realignment. -[ensemble]: http://bcbio.wordpress.com/2013/10/21/updated-comparison-of-variant-detection-methods-ensemble-freebayes-and-minimal-bam-preparation-pipelines/ +[ensemble]: http://bcb.io/2013/10/21/updated-comparison-of-variant-detection-methods-ensemble-freebayes-and-minimal-bam-preparation-pipelines/ [bcbio.variation.recall]: https://github.com/chapmanb/bcbio.variation.recall - Add in methylation analysis approaches. See diff --git a/docs/contents/installation.rst b/docs/contents/installation.rst index 12630cb36..8d3d313a3 100644 --- a/docs/contents/installation.rst +++ b/docs/contents/installation.rst @@ -286,7 +286,7 @@ for commercial usage. .. _VEP: http://www.ensembl.org/info/docs/tools/vep/index.html .. _GATK download: http://www.broadinstitute.org/gatk/download .. _a distribution of GATK for commercial users: http://www.appistry.com/gatk -.. _FreeBayes and GATK comparison: http://bcbio.wordpress.com/2013/10/21/updated-comparison-of-variant-detection-methods-ensemble-freebayes-and-minimal-bam-preparation-pipelines/ +.. _FreeBayes and GATK comparison: http://bcb.io/2013/10/21/updated-comparison-of-variant-detection-methods-ensemble-freebayes-and-minimal-bam-preparation-pipelines/ kraken ~~~~~~ diff --git a/docs/contents/parallel.rst b/docs/contents/parallel.rst index 0740acf1f..cf7464263 100644 --- a/docs/contents/parallel.rst +++ b/docs/contents/parallel.rst @@ -252,6 +252,6 @@ contribute your tips and thoughts. We found the biggest initial factor limiting scaling was network bandwidth between compute and storage nodes. -.. _post on scaling bcbio-nextgen: http://bcbio.wordpress.com/2013/05/22/scaling-variant-detection-pipelines-for-whole-genome-sequencing-analysis/ +.. _post on scaling bcbio-nextgen: http://bcb.io/2013/05/22/scaling-variant-detection-pipelines-for-whole-genome-sequencing-analysis/ .. _Harvard FAS Research Computing: http://rc.fas.harvard.edu/ .. _Dell's Active Infrastructure for Life Sciences: http://dell.com/ai-hpc-lifesciences diff --git a/docs/contents/presentations.rst b/docs/contents/presentations.rst index a6d7e9493..8e97a0289 100644 --- a/docs/contents/presentations.rst +++ b/docs/contents/presentations.rst @@ -145,9 +145,9 @@ Links from the presentation .. _Conda: http://www.continuum.io/blog/conda .. _documentation: bcbio-nextgen.readthedocs.org .. _Arvados framework: https://arvados.org/ -.. _improved scaling for NGS workflows: http://bcbio.wordpress.com/2013/05/22/scaling-variant-detection-pipelines-for-whole-genome-sequencing-analysis/ -.. _aligners and callers: http://bcbio.wordpress.com/2013/05/06/framework-for-evaluating-variant-detection-methods-comparison-of-aligners-and-callers/ -.. _minimal BAM preparation workflows: http://bcbio.wordpress.com/2013/10/21/updated-comparison-of-variant-detection-methods-ensemble-freebayes-and-minimal-bam-preparation-pipelines/ +.. _improved scaling for NGS workflows: http://bcb.io/2013/05/22/scaling-variant-detection-pipelines-for-whole-genome-sequencing-analysis/ +.. _aligners and callers: http://bcb.io/2013/05/06/framework-for-evaluating-variant-detection-methods-comparison-of-aligners-and-callers/ +.. _minimal BAM preparation workflows: http://bcb.io/2013/10/21/updated-comparison-of-variant-detection-methods-ensemble-freebayes-and-minimal-bam-preparation-pipelines/ .. _Coverage assessment: https://github.com/chapmanb/bcbio.coverage .. _Mt Sinai workshop website: http://www.hpcwire.com/event/strategies-accelerating-genomic-sequencing-pipeline/ .. _Mt Sinai workshop slides: https://github.com/chapmanb/bcbb/raw/master/talks/mtsinai2013_bcbio_nextgen/chapman_mtsinai_bcbio.pdf diff --git a/docs/contents/testing.rst b/docs/contents/testing.rst index 2a0dda662..a4e658cda 100644 --- a/docs/contents/testing.rst +++ b/docs/contents/testing.rst @@ -147,7 +147,7 @@ Finally run the analysis, distributed on 8 local cores, with:: The ``grading-summary.csv`` contains detailed comparisons of the results to the NIST reference materials, enabling rapid comparisons of methods. -.. _combined ensemble callset: http://bcbio.wordpress.com/2013/02/06/an-automated-ensemble-method-for-combining-and-evaluating-genomic-variants-from-multiple-callers/ +.. _combined ensemble callset: http://bcb.io/2013/02/06/an-automated-ensemble-method-for-combining-and-evaluating-genomic-variants-from-multiple-callers/ .. _Genome in a Bottle: http://www.genomeinabottle.org/ .. _EdgeBio's: http://www.edgebio.com/ @@ -292,7 +292,7 @@ information about the pipeline. To run the analysis: .. _Platinum genomes project: http://www.illumina.com/platinumgenomes/ .. _NA12878-illumina.yaml: https://raw.github.com/chapmanb/bcbio-nextgen/master/config/examples/NA12878-illumina.yaml -.. _blog post on whole genome scaling: http://bcbio.wordpress.com/2013/05/22/scaling-variant-detection-pipelines-for-whole-genome-sequencing-analysis/ +.. _blog post on whole genome scaling: http://bcb.io/2013/05/22/scaling-variant-detection-pipelines-for-whole-genome-sequencing-analysis/ Test suite