Update documentation links to bcb.io

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
 -----------

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

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
 ~~~~~~

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

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

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