From 3578e489a77072db627c55269a213c59b4d0c9cb Mon Sep 17 00:00:00 2001 From: sigven Date: Tue, 27 Nov 2018 17:34:36 +0100 Subject: [PATCH] 0.7.0 --- README.md | 22 +++++++------- docs/CHANGELOG.md | 2 +- docs/CHANGELOG.rst | 4 +-- docs/_build/doctrees/CHANGELOG.doctree | Bin 80003 -> 79961 bytes docs/_build/doctrees/environment.pickle | Bin 42561 -> 42531 bytes docs/_build/doctrees/getting_started.doctree | Bin 47632 -> 47687 bytes docs/_build/html/CHANGELOG.html | 6 ++-- docs/_build/html/_sources/CHANGELOG.rst.txt | 4 +-- .../html/_sources/getting_started.rst.txt | 26 ++++++++-------- docs/_build/html/getting_started.html | 28 +++++++++--------- docs/_build/html/index.html | 2 +- docs/_build/html/searchindex.js | 2 +- docs/getting_started.md | 18 +++++------ docs/getting_started.rst | 26 ++++++++-------- pcgr.py | 2 +- 15 files changed, 71 insertions(+), 71 deletions(-) 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 a3b32d03ce92685d4ea62f752608a2a93c9cd5aa..61b6d67ac7e12739ae6aa89119fc6f5778e2f712 100644 GIT binary patch delta 146 zcmZqv$a3=o3rhpbRE~`-?Tosj272at1`4_ge)(kzM&>0M3PuKo7E?0VW2a<@_Mpjb zKE>$hr@@<-U#1IEstZ<{n4t(%s~kH8p&FW+(#9P>!8~#T1}QpkCOJX{Wm3orYP0=DL8q{ck6b0G_D4G;5+yF&_0BK#gsTsvG%xIU${;~JobIyF{JKy_!=gc{u-}UoHesvrFh5NjYX|-49jP@PN zb=oUN+mFKOj|En%`Fy76%hB;KME9cEaHrnsL<`|q(`opwVKgl_3eV2}m}j`&yk{-n zG1~L4;TgKyFz3O#6AJVA z_s~VDNKhSh?ij9XHPO+%DBSHCe!!?3tG?0pET`>7x1w;QrMH&@ec7Njw%)2;)Y}ci ztz9g+uJefUGQ8^r0_f`0q9(FRNO0E0vG 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SYCK-IKXCVd5CrD=m$u&%eaJBY 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
      -
    • dev/unreleased - Nov 19th 2018
        +
      • 0.7.0 - Nov 27th 2018
        • Fixed
        • Added
        • Changed
          • @@ -184,8 +184,8 @@

          CHANGELOG

          -
          -

          dev/unreleased - Nov 19th 2018

          +
          +

          0.7.0 - Nov 27th 2018

          Fixed

            diff --git a/docs/_build/html/_sources/CHANGELOG.rst.txt b/docs/_build/html/_sources/CHANGELOG.rst.txt index e85852a1..6b953f8f 100644 --- a/docs/_build/html/_sources/CHANGELOG.rst.txt +++ b/docs/_build/html/_sources/CHANGELOG.rst.txt @@ -1,8 +1,8 @@ CHANGELOG --------- -dev/unreleased - Nov 19th 2018 -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +0.7.0 - Nov 27th 2018 +^^^^^^^^^^^^^^^^^^^^^ Fixed ''''' diff --git a/docs/_build/html/_sources/getting_started.rst.txt b/docs/_build/html/_sources/getting_started.rst.txt index b61c1298..f93dc826 100644 --- a/docs/_build/html/_sources/getting_started.rst.txt +++ b/docs/_build/html/_sources/getting_started.rst.txt @@ -70,26 +70,26 @@ Latest release ^^^^^^^^^^^^^^ a. Download and unpack the `latest software release - (0.6.2.1) `__ + (0.7.0) `__ b. Download and unpack the assembly-specific data bundle in the PCGR directory - - `grch37 data - bundle `__ - (approx 9.2Gb) - - `grch38 data - bundle `__ - (approx 13Gb) + - `grch37 data bundle - + 20181119 `__ + (approx 9Gb) + - `grch38 data bundle - + 20181119 `__ + (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) `__ from DockerHub + (0.7.0) `__ from DockerHub (approx 5.1Gb): - - ``docker pull sigven/pcgr:0.6.2.1`` (PCGR annotation engine) + - ``docker pull sigven/pcgr:0.7.0`` (PCGR annotation engine) STEP 3: Input preprocessing ~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -178,7 +178,7 @@ A tumor sample report is generated by calling the Python script 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) @@ -215,9 +215,9 @@ configuration files customized for these samples. 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/_build/html/getting_started.html b/docs/_build/html/getting_started.html index b2b4a8be..40b04e4a 100644 --- a/docs/_build/html/getting_started.html +++ b/docs/_build/html/getting_started.html @@ -239,18 +239,18 @@

            Development version

            Latest release

              -

            1. Download and unpack the latest software release -(0.6.2.1)

              +

            2. Download and unpack the latest software release +(0.7.0)

            3. Download and unpack the assembly-specific data bundle in the PCGR directory

              @@ -258,10 +258,10 @@

              Latest releasePull the PCGR Docker image -(0.6.2.1) from DockerHub +(0.7.0) from DockerHub (approx 5.1Gb):

                -
              • docker pull sigven/pcgr:0.6.2.1 (PCGR annotation engine)
                • +
              • docker pull sigven/pcgr:0.7.0 (PCGR annotation engine)

            @@ -346,7 +346,7 @@

            STEP 5: Run examplepython 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/_build/html/index.html b/docs/_build/html/index.html index f7d961d4..f2a88f34 100644 --- a/docs/_build/html/index.html +++ b/docs/_build/html/index.html @@ -207,7 +207,7 @@

              Welcome to Personal Cancer Genome Reporter’s documentation!CHANGELOG
                -
              • dev/unreleased - Nov 19th 2018
                • +
              • 0.7.0 - Nov 27th 2018
              • 0.6.2.1 - May 14th 2018
              • 0.6.2 - May 9th 2018
              • 0.6.1 - May 2nd 2018
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\ No newline at end of file diff --git a/docs/getting_started.md b/docs/getting_started.md index 1836e448..66579c21 100644 --- a/docs/getting_started.md +++ b/docs/getting_started.md @@ -33,15 +33,15 @@ 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](https://drive.google.com/open?id=1cGBAmAh5t4miIeRrrd0zHsPCFToOr0Lf) (approx 9.2Gb) - * [grch38 data bundle](https://drive.google.com/open?id=1CZNc87E0K5AK2RDSNU57FqLp0H1skpUh) (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 @@ -106,7 +106,7 @@ 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) @@ -141,9 +141,9 @@ 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 samples. 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/getting_started.rst b/docs/getting_started.rst index b61c1298..f93dc826 100644 --- a/docs/getting_started.rst +++ b/docs/getting_started.rst @@ -70,26 +70,26 @@ Latest release ^^^^^^^^^^^^^^ a. Download and unpack the `latest software release - (0.6.2.1) `__ + (0.7.0) `__ b. Download and unpack the assembly-specific data bundle in the PCGR directory - - `grch37 data - bundle `__ - (approx 9.2Gb) - - `grch38 data - bundle `__ - (approx 13Gb) + - `grch37 data bundle - + 20181119 `__ + (approx 9Gb) + - `grch38 data bundle - + 20181119 `__ + (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) `__ from DockerHub + (0.7.0) `__ from DockerHub (approx 5.1Gb): - - ``docker pull sigven/pcgr:0.6.2.1`` (PCGR annotation engine) + - ``docker pull sigven/pcgr:0.7.0`` (PCGR annotation engine) STEP 3: Input preprocessing ~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -178,7 +178,7 @@ A tumor sample report is generated by calling the Python script 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) @@ -215,9 +215,9 @@ configuration files customized for these samples. 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/pcgr.py b/pcgr.py index 79d15c5a..6c756e55 100755 --- a/pcgr.py +++ b/pcgr.py @@ -11,7 +11,7 @@ import platform import toml -pcgr_version = 'dev' +pcgr_version = '0.7.0' db_version = 'PCGR_DB_VERSION = 20181119' vep_version = '94' global vep_assembly