diff --git a/README.md b/README.md index cb9a5cab..4d475302 100755 --- a/README.md +++ b/README.md @@ -7,8 +7,8 @@ The Personal Cancer Genome Reporter (PCGR) is a stand-alone software package for ![PCGR overview](PCGR_workflow.png) ### News -* _Nov 19th 2018_: - * Dev version is available for download (installation instructions below) +* _Nov 27th 2018_: **0.7.0 release** + * Bundle update and bug fixing (see [CHANGELOG](http://pcgr.readthedocs.io/en/latest/CHANGELOG.html#nov-27th-2018) ) * Reporting germline variants for cancer predisposition? Check out [github.com/sigven/cpsr](https://github.com/sigven/cpsr) * _May 14th 2018_: **0.6.2.1 release** * [CHANGELOG](http://pcgr.readthedocs.io/en/latest/CHANGELOG.html#may-14th-2018) @@ -109,17 +109,17 @@ c. Pull the [PCGR Docker image (*dev*)](https://hub.docker.com/r/sigven/pcgr/) f ##### Latest release -a. Download and unpack the [latest software release (0.6.2.1)](https://github.com/sigven/pcgr/releases/tag/v6.2.1) +a. Download and unpack the [latest software release (0.7.0)](https://github.com/sigven/pcgr/releases/tag/v0.7.0) b. Download and unpack the assembly-specific data bundle in the PCGR directory - * [grch37 data bundle - 20180509](https://drive.google.com/open?id=1cGBAmAh5t4miIeRrrd0zHsPCFToOr0Lf) (approx 9.2Gb) - * [grch38 data bundle - 20180509](https://drive.google.com/open?id=12q3rr7xpdBfaefRi0ysFHbH34kehNZOV) (approx 13Gb) + * [grch37 data bundle - 20181119](https://drive.google.com/open?id=1OL5C994HDaeadASz7KzMhPoXfdSiyhNy) (approx 9Gb) + * [grch38 data bundle - 20181119](https://drive.google.com/open?id=1CZNc87E0K5AK2RDSNU57FqLp0H1skpUh) (approx 14Gb) * *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 -c. 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) +c. Pull the [PCGR Docker image (0.7.0)](https://hub.docker.com/r/sigven/pcgr/) from DockerHub (approx 5.1Gb): + * `docker pull sigven/pcgr:0.7.0` (PCGR annotation engine) #### STEP 3: Input preprocessing @@ -182,7 +182,7 @@ 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-0.6.2.1 + e.g. ~/pcgr-0.7.0 output_dir Output directory {grch37,grch38} Genome assembly build: grch37 or grch38 configuration_file PCGR configuration file (TOML format) @@ -218,9 +218,9 @@ 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-0.6.2.1/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` +`python pcgr.py --input_vcf ~/pcgr-0.7.0/examples/tumor_sample.COAD.vcf.gz` +`--input_cna ~/pcgr-0.7.0/examples/tumor_sample.COAD.cna.tsv` +` ~/pcgr-0.7.0 ~/pcgr-0.7.0/examples grch37 ~/pcgr-0.7.0/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 6b9078e5..b038e26f 100644 --- a/docs/CHANGELOG.md +++ b/docs/CHANGELOG.md @@ -1,7 +1,7 @@ ## CHANGELOG -#### dev/unreleased - Nov 19th 2018 +#### 0.7.0 - Nov 27th 2018 ##### Fixed * Bug in assignment of variants to tier1/tier2 [Issue #61](https://github.com/sigven/pcgr/issues/61) diff --git a/docs/CHANGELOG.rst b/docs/CHANGELOG.rst index e85852a1..6b953f8f 100644 --- a/docs/CHANGELOG.rst +++ b/docs/CHANGELOG.rst @@ -1,8 +1,8 @@ CHANGELOG --------- -dev/unreleased - Nov 19th 2018 -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +0.7.0 - Nov 27th 2018 +^^^^^^^^^^^^^^^^^^^^^ Fixed ''''' diff --git a/docs/_build/doctrees/CHANGELOG.doctree b/docs/_build/doctrees/CHANGELOG.doctree index a3b32d03..61b6d67a 100644 Binary files a/docs/_build/doctrees/CHANGELOG.doctree and b/docs/_build/doctrees/CHANGELOG.doctree differ diff --git a/docs/_build/doctrees/environment.pickle b/docs/_build/doctrees/environment.pickle index 0fae1f79..f0c7cdcb 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 126109e7..14fc3018 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/CHANGELOG.html b/docs/_build/html/CHANGELOG.html index def05d1e..4dbd9e0e 100644 --- a/docs/_build/html/CHANGELOG.html +++ b/docs/_build/html/CHANGELOG.html @@ -91,7 +91,7 @@
  • Output
  • Tier models
  • CHANGELOG