diff --git a/README.md b/README.md index 699fe412..10dcb28a 100755 --- a/README.md +++ b/README.md @@ -7,6 +7,8 @@ The Personal Cancer Genome Reporter (PCGR) is a stand-alone software package for ![PCGR overview](PCGR_workflow.png) ### News +* _May 14th 2018_: **0.6.2.1 release** + * [CHANGELOG](http://pcgr.readthedocs.io/en/latest/CHANGELOG.html#may-14th-2018) * _May 9th 2018_: **0.6.2 release** * Fixed various bugs reported by users (see [CHANGELOG](http://pcgr.readthedocs.io/en/latest/CHANGELOG.html#may-9th-2018)) * Data bundle update (ClinVar, KEGG, CIViC, UniProt, DiseaseOntology) @@ -37,8 +39,8 @@ The Personal Cancer Genome Reporter (PCGR) is a stand-alone software package for ### Example reports -* [Report for a breast tumor sample (TCGA)](http://folk.uio.no/sigven/tumor_sample.BRCA.pcgr_acmg.grch37.0.6.2.html) -* [Report for a colon adenocarcinoma sample (TCGA)](http://folk.uio.no/sigven/tumor_sample.COAD.pcgr_acmg.grch37.0.6.2.html) +* [Report for a breast tumor sample (TCGA)](http://folk.uio.no/sigven/tumor_sample.BRCA.pcgr_acmg.grch37.0.6.2.1.html) +* [Report for a colon adenocarcinoma sample (TCGA)](http://folk.uio.no/sigven/tumor_sample.COAD.pcgr_acmg.grch37.0.6.2.1.html) ### PCGR documentation @@ -49,7 +51,7 @@ If you use PCGR, please cite our recent publication: Sigve Nakken, Ghislain Fournous, Daniel Vodák, Lars Birger Aaasheim, Ola Myklebost, and Eivind Hovig. __Personal Cancer Genome Reporter: variant interpretation report for precision oncology__ (2017). _Bioinformatics_. 34(10):1778–1780. doi:[10.1093/bioinformatics/btx817](https://doi.org/10.1093/bioinformatics/btx817) -### Annotation resources included in PCGR (0.6.2) +### Annotation resources included in PCGR (0.6.2.1) * [VEP v92](http://www.ensembl.org/info/docs/tools/vep/index.html) - Variant Effect Predictor release 92 (GENCODE v28/v19 as the gene reference dataset) * [CIViC](http://civic.genome.wustl.edu) - Clinical interpretations of variants in cancer (May 8th 2018) @@ -88,15 +90,15 @@ An installation of Python (version _3.6_) is required to run PCGR. Check that Py #### STEP 2: Download PCGR and data bundle -1. Download and unpack the [latest software release (0.6.2)](https://github.com/sigven/pcgr/releases/tag/v0.6.2) +1. Download and unpack the [latest software release (0.6.2.1)](https://github.com/sigven/pcgr/releases/tag/v0.6.2.1) 2. Download and unpack the assembly-specific data bundle in the PCGR directory * [grch37 data bundle](https://drive.google.com/open?id=1cGBAmAh5t4miIeRrrd0zHsPCFToOr0Lf) (approx 9Gb) * [grch38 data bundle](https://drive.google.com/open?id=12q3rr7xpdBfaefRi0ysFHbH34kehNZOV) (approx 9Gb) * *Unpacking*: `gzip -dc pcgr.databundle.grch37.YYYYMMDD.tgz | tar xvf -` A _data/_ folder within the _pcgr-X.X_ software folder should now have been produced -3. Pull the [PCGR Docker image (0.6.2)](https://hub.docker.com/r/sigven/pcgr/) from DockerHub (approx 5.1Gb): - * `docker pull sigven/pcgr:0.6.2` (PCGR annotation engine) +3. Pull the [PCGR Docker image (0.6.2.1)](https://hub.docker.com/r/sigven/pcgr/) from DockerHub (approx 5.1Gb): + * `docker pull sigven/pcgr:0.6.2.1` (PCGR annotation engine) #### STEP 3: Input preprocessing @@ -157,7 +159,7 @@ A tumor sample report is generated by calling the Python script __pcgr.py__, whi positional arguments: pcgr_dir PCGR base directory with accompanying data directory, - e.g. ~/pcgr-0.6.2 + e.g. ~/pcgr-0.6.2.1 output_dir Output directory {grch37,grch38} Genome assembly build: grch37 or grch38 configuration_file PCGR configuration file (TOML format) @@ -186,9 +188,9 @@ A tumor sample report is generated by calling the Python script __pcgr.py__, whi The _examples_ folder contain input files from two tumor samples sequenced within TCGA (**GRCh37** only). It also contains PCGR configuration files customized for these cases. A report for a colorectal tumor case can be generated by running the following command in your terminal window: -`python pcgr.py --input_vcf ~/pcgr-0.6.2/examples/tumor_sample.COAD.vcf.gz` -`--input_cna ~/pcgr-0.6.2/examples/tumor_sample.COAD.cna.tsv` -` ~/pcgr-0.6.2 ~/pcgr-0.6.2/examples grch37 ~/pcgr-0.6.2/examples/pcgr_conf.COAD.toml tumor_sample.COAD` +`python pcgr.py --input_vcf ~/pcgr-0.6.2.1/examples/tumor_sample.COAD.vcf.gz` +`--input_cna ~/pcgr-0.6.2.1/examples/tumor_sample.COAD.cna.tsv` +` ~/pcgr-0.6.2.1 ~/pcgr-0.6.2.1/examples grch37 ~/pcgr-0.6.2.1/examples/pcgr_conf.COAD.toml tumor_sample.COAD` This command will run the Docker-based PCGR workflow and produce the following output files in the _examples_ folder: diff --git a/docs/CHANGELOG.md b/docs/CHANGELOG.md index 8c3a48d2..cfc831ca 100644 --- a/docs/CHANGELOG.md +++ b/docs/CHANGELOG.md @@ -1,6 +1,12 @@ ## CHANGELOG +#### 0.6.2.1 - May 14th 2018 + +##### Fixed + + * Bug in copy number annotation (broad/focal) + #### 0.6.2 - May 9th 2018 ##### Fixed diff --git a/docs/CHANGELOG.rst b/docs/CHANGELOG.rst index de6ee8ac..0d07b562 100644 --- a/docs/CHANGELOG.rst +++ b/docs/CHANGELOG.rst @@ -1,6 +1,14 @@ CHANGELOG --------- +0.6.2.1 - May 14th 2018 +^^^^^^^^^^^^^^^^^^^^^^^ + +Fixed +''''' + +- Bug in copy number annotation (broad/focal) + 0.6.2 - May 9th 2018 ^^^^^^^^^^^^^^^^^^^^ diff --git a/docs/_build/doctrees/CHANGELOG.doctree b/docs/_build/doctrees/CHANGELOG.doctree index a5a78ecf..fbc5dc31 100644 Binary files a/docs/_build/doctrees/CHANGELOG.doctree and b/docs/_build/doctrees/CHANGELOG.doctree differ diff --git a/docs/_build/doctrees/about.doctree b/docs/_build/doctrees/about.doctree index a90c039e..c3259a3b 100644 Binary files a/docs/_build/doctrees/about.doctree and b/docs/_build/doctrees/about.doctree differ diff --git a/docs/_build/doctrees/environment.pickle b/docs/_build/doctrees/environment.pickle index afb3190f..13e22d2b 100644 Binary files a/docs/_build/doctrees/environment.pickle and b/docs/_build/doctrees/environment.pickle differ diff --git a/docs/_build/doctrees/getting_started.doctree b/docs/_build/doctrees/getting_started.doctree index 6e552637..7e0c48c7 100644 Binary files a/docs/_build/doctrees/getting_started.doctree and b/docs/_build/doctrees/getting_started.doctree differ diff --git a/docs/_build/html/.buildinfo b/docs/_build/html/.buildinfo index d89c780b..29bc0b13 100644 --- a/docs/_build/html/.buildinfo +++ b/docs/_build/html/.buildinfo @@ -1,4 +1,4 @@ # Sphinx build info version 1 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. -config: 04616fa05efaaa19416d1091e820f76a +config: c0c8197050de327e0bb0458a914594e7 tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/docs/_build/html/CHANGELOG.html b/docs/_build/html/CHANGELOG.html index 2b647c6e..8bd8877a 100644 --- a/docs/_build/html/CHANGELOG.html +++ b/docs/_build/html/CHANGELOG.html @@ -8,7 +8,7 @@ - CHANGELOG — Personal Cancer Genome Reporter 0.6.2 documentation + CHANGELOG — Personal Cancer Genome Reporter 0.6.2.1 documentation @@ -35,7 +35,7 @@ - + @@ -64,7 +64,7 @@
- 0.6.2 + 0.6.2.1
@@ -94,17 +94,21 @@
  • Output
  • Tier models
  • CHANGELOG