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22 changes: 11 additions & 11 deletions README.md
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Expand Up @@ -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)
Expand Down Expand Up @@ -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

Expand Down Expand Up @@ -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)
Expand Down Expand Up @@ -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:
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2 changes: 1 addition & 1 deletion docs/CHANGELOG.md
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@@ -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)
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@@ -1,8 +1,8 @@
CHANGELOG
---------

dev/unreleased - Nov 19th 2018
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
0.7.0 - Nov 27th 2018
^^^^^^^^^^^^^^^^^^^^^

Fixed
'''''
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6 changes: 3 additions & 3 deletions docs/_build/html/CHANGELOG.html
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Expand Up @@ -91,7 +91,7 @@
<li class="toctree-l1"><a class="reference internal" href="output.html">Output</a></li>
<li class="toctree-l1"><a class="reference internal" href="tier_systems.html">Tier models</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="#">CHANGELOG</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#dev-unreleased-nov-19th-2018">dev/unreleased - Nov 19th 2018</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#nov-27th-2018">0.7.0 - Nov 27th 2018</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#fixed">Fixed</a></li>
<li class="toctree-l3"><a class="reference internal" href="#added">Added</a></li>
<li class="toctree-l3"><a class="reference internal" href="#changed">Changed</a></li>
Expand Down Expand Up @@ -184,8 +184,8 @@

<div class="section" id="changelog">
<h1>CHANGELOG<a class="headerlink" href="#changelog" title="Permalink to this headline"></a></h1>
<div class="section" id="dev-unreleased-nov-19th-2018">
<h2>dev/unreleased - Nov 19th 2018<a class="headerlink" href="#dev-unreleased-nov-19th-2018" title="Permalink to this headline"></a></h2>
<div class="section" id="nov-27th-2018">
<h2>0.7.0 - Nov 27th 2018<a class="headerlink" href="#nov-27th-2018" title="Permalink to this headline"></a></h2>
<div class="section" id="fixed">
<h3>Fixed<a class="headerlink" href="#fixed" title="Permalink to this headline"></a></h3>
<ul class="simple">
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4 changes: 2 additions & 2 deletions docs/_build/html/_sources/CHANGELOG.rst.txt
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@@ -1,8 +1,8 @@
CHANGELOG
---------

dev/unreleased - Nov 19th 2018
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
0.7.0 - Nov 27th 2018
^^^^^^^^^^^^^^^^^^^^^

Fixed
'''''
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26 changes: 13 additions & 13 deletions docs/_build/html/_sources/getting_started.rst.txt
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Expand Up @@ -70,26 +70,26 @@ Latest release
^^^^^^^^^^^^^^

a. Download and unpack the `latest software release
(0.6.2.1) <https://github.com/sigven/pcgr/releases/tag/v6.2.1>`__
(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
(0.7.0) <https://hub.docker.com/r/sigven/pcgr/>`__ 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
~~~~~~~~~~~~~~~~~~~~~~~~~~~
Expand Down Expand Up @@ -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)
Expand Down Expand Up @@ -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:
Expand Down
28 changes: 14 additions & 14 deletions docs/_build/html/getting_started.html
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Expand Up @@ -239,29 +239,29 @@ <h3>Development version<a class="headerlink" href="#development-version" title="
<div class="section" id="latest-release">
<h3>Latest release<a class="headerlink" href="#latest-release" title="Permalink to this headline"></a></h3>
<ol class="loweralpha">
<li><p class="first">Download and unpack the <a class="reference external" href="https://github.com/sigven/pcgr/releases/tag/v6.2.1">latest software release
(0.6.2.1)</a></p>
<li><p class="first">Download and unpack the <a class="reference external" href="https://github.com/sigven/pcgr/releases/tag/v0.7.0">latest software release
(0.7.0)</a></p>
</li>
<li><p class="first">Download and unpack the assembly-specific data bundle in the PCGR
directory</p>
<ul class="simple">
<li><a class="reference external" href="https://drive.google.com/open?id=1cGBAmAh5t4miIeRrrd0zHsPCFToOr0Lf">grch37 data
bundle</a>
(approx 9.2Gb)</li>
<li><a class="reference external" href="https://drive.google.com/open?id=1CZNc87E0K5AK2RDSNU57FqLp0H1skpUh">grch38 data
bundle</a>
(approx 13Gb)</li>
<li><a class="reference external" href="https://drive.google.com/open?id=1OL5C994HDaeadASz7KzMhPoXfdSiyhNy">grch37 data bundle -
20181119</a>
(approx 9Gb)</li>
<li><a class="reference external" href="https://drive.google.com/open?id=1CZNc87E0K5AK2RDSNU57FqLp0H1skpUh">grch38 data bundle -
20181119</a>
(approx 14Gb)</li>
<li><em>Unpacking</em>:
<code class="docutils literal notranslate"><span class="pre">gzip</span> <span class="pre">-dc</span> <span class="pre">pcgr.databundle.grch37.YYYYMMDD.tgz</span> <span class="pre">|</span> <span class="pre">tar</span> <span class="pre">xvf</span> <span class="pre">-</span></code></li>
</ul>
<p>A <em>data/</em> folder within the <em>pcgr-X.X</em> software folder should now
have been produced</p>
</li>
<li><p class="first">Pull the <a class="reference external" href="https://hub.docker.com/r/sigven/pcgr/">PCGR Docker image
(0.6.2.1)</a> from DockerHub
(0.7.0)</a> from DockerHub
(approx 5.1Gb):</p>
<ul class="simple">
<li><code class="docutils literal notranslate"><span class="pre">docker</span> <span class="pre">pull</span> <span class="pre">sigven/pcgr:0.6.2.1</span></code> (PCGR annotation engine)</li>
<li><code class="docutils literal notranslate"><span class="pre">docker</span> <span class="pre">pull</span> <span class="pre">sigven/pcgr:0.7.0</span></code> (PCGR annotation engine)</li>
</ul>
</li>
</ol>
Expand Down Expand Up @@ -346,7 +346,7 @@ <h2>STEP 5: Run example<a class="headerlink" href="#step-5-run-example" title="P

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)
Expand Down Expand Up @@ -383,9 +383,9 @@ <h2>STEP 5: Run example<a class="headerlink" href="#step-5-run-example" title="P
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:</p>
<p><code class="docutils literal notranslate"><span class="pre">python</span> <span class="pre">pcgr.py</span> <span class="pre">--input_vcf</span> <span class="pre">~/pcgr-0.6.2.1/examples/tumor_sample.COAD.vcf.gz</span></code>
<code class="docutils literal notranslate"><span class="pre">--input_cna</span> <span class="pre">~/pcgr-0.6.2.1/examples/tumor_sample.COAD.cna.tsv</span></code>
<code class="docutils literal notranslate"><span class="pre">~/pcgr-0.6.2.1</span> <span class="pre">~/pcgr-0.6.2.1/examples</span> <span class="pre">grch37</span> <span class="pre">~/pcgr-0.6.2.1/examples/pcgr_conf.COAD.toml</span> <span class="pre">tumor_sample.COAD</span></code></p>
<p><code class="docutils literal notranslate"><span class="pre">python</span> <span class="pre">pcgr.py</span> <span class="pre">--input_vcf</span> <span class="pre">~/pcgr-0.7.0/examples/tumor_sample.COAD.vcf.gz</span></code>
<code class="docutils literal notranslate"><span class="pre">--input_cna</span> <span class="pre">~/pcgr-0.7.0/examples/tumor_sample.COAD.cna.tsv</span></code>
<code class="docutils literal notranslate"><span class="pre">~/pcgr-0.7.0</span> <span class="pre">~/pcgr-0.7.0/examples</span> <span class="pre">grch37</span> <span class="pre">~/pcgr-0.7.0/examples/pcgr_conf.COAD.toml</span> <span class="pre">tumor_sample.COAD</span></code></p>
<p>This command will run the Docker-based PCGR workflow and produce the
following output files in the <em>examples</em> folder:</p>
<ol class="arabic simple">
Expand Down
2 changes: 1 addition & 1 deletion docs/_build/html/index.html
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Expand Up @@ -207,7 +207,7 @@ <h1>Welcome to Personal Cancer Genome Reporter’s documentation!<a class="heade
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="CHANGELOG.html">CHANGELOG</a><ul>
<li class="toctree-l2"><a class="reference internal" href="CHANGELOG.html#dev-unreleased-nov-19th-2018">dev/unreleased - Nov 19th 2018</a></li>
<li class="toctree-l2"><a class="reference internal" href="CHANGELOG.html#nov-27th-2018">0.7.0 - Nov 27th 2018</a></li>
<li class="toctree-l2"><a class="reference internal" href="CHANGELOG.html#may-14th-2018">0.6.2.1 - May 14th 2018</a></li>
<li class="toctree-l2"><a class="reference internal" href="CHANGELOG.html#may-9th-2018">0.6.2 - May 9th 2018</a></li>
<li class="toctree-l2"><a class="reference internal" href="CHANGELOG.html#may-2nd-2018">0.6.1 - May 2nd 2018</a></li>
Expand Down
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18 changes: 9 additions & 9 deletions docs/getting_started.md
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Expand Up @@ -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

Expand Down Expand Up @@ -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)
Expand Down Expand Up @@ -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:
Expand Down
26 changes: 13 additions & 13 deletions docs/getting_started.rst
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Expand Up @@ -70,26 +70,26 @@ Latest release
^^^^^^^^^^^^^^

a. Download and unpack the `latest software release
(0.6.2.1) <https://github.com/sigven/pcgr/releases/tag/v6.2.1>`__
(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
(0.7.0) <https://hub.docker.com/r/sigven/pcgr/>`__ 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
~~~~~~~~~~~~~~~~~~~~~~~~~~~
Expand Down Expand Up @@ -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)
Expand Down Expand Up @@ -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:
Expand Down
2 changes: 1 addition & 1 deletion pcgr.py
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Expand Up @@ -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
Expand Down

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