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Ac readqc tutorial #386

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Jan 18, 2018
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2 changes: 2 additions & 0 deletions doc/Makefile
Original file line number Diff line number Diff line change
@@ -48,6 +48,7 @@ images/%.svg: ../CGATPipelines/%.py
html: build-images
rm -f ../{CGATPipelines,scripts}/*.pyc
$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) _build/html
cp -r images/ _build/html/
@echo
@echo "Build finished. The HTML pages are in _build/html."

@@ -112,5 +113,6 @@ publish:
chmod -R a+x $(DIR_PUBLISH)
chmod -R a+r $(DIR_PUBLISH)
@echo "fixing URLs"
cp images/ $(DIR_PUBLISH)
find $(DIR_PUBLISH)/ -name "*.html" -exec \
perl -p -i -e $(URL_SUB) {} \;
2 changes: 1 addition & 1 deletion doc/PipelinesBackground.rst
Original file line number Diff line number Diff line change
@@ -56,7 +56,7 @@ associated with ChIP-seq.

**Below is a flow and organisation of our production piplines:**

.. image:: ../../images/Figure_for_documentation.png
.. image:: images/Figure_for_documentation.png
:height: 1000px
:width: 2000 px
:scale: 50%
13 changes: 11 additions & 2 deletions doc/Tutorials.rst
Original file line number Diff line number Diff line change
@@ -24,7 +24,7 @@ The functionality and the third-party software that they wrap are detailed below

**A summary of what each pipeline does is shown below:**

.. image:: ../../images/Slide2.png
.. image:: images/Figure_pipelines.png
:height: 1000px
:width: 1000 px
:scale: 50%
@@ -67,6 +67,15 @@ does not need to be modified. To run the pipeline do the following::
This ``--local`` will run the pipeline locally if you do not have access to a cluster. Alternatively if you have a
cluster remove the ``--local`` option and the pipleine will distribute your jobs accross the cluster.

.. note::

If you get the following sqlite error while running the pipeline please continue running the pipeline with a
single process as follows ``cgatflow readqc make full -v5 -p1 --local`` and the pipeline should complete without
errors. This occurrs because sqlite cannot handle multi-threaded access. Although we have added a fix for most
cases, this can sometimes not always work.



**4.** The **final step** is to generate the report. We have a preference for multiqc, however we also have our own
CGAT report implimented in this pipeline. To generate the reports run the command::

@@ -447,4 +456,4 @@ Conclusion

These three tutorials are designed to give users a flavour of how to run our upstream NGS production pipelines.It is hoped that
once familiar with the workflows and design of our pipelines users will be encouraged to cotribute to the code development, the
code is constant development and we look forward for new users to incorporate these pipelines in their analysis.
code is constant development and we look forward for new users to incorporate these pipelines in their analysis.
File renamed without changes