New upstream version 0.11.2

            docker run --rm -t \

                -e HDF5="${HDF5:-install}" \

                -e H5_CFLAGS="${H5_CFLAGS}" \

                -e HDF5_VERSION="1.10.4" \

                -e H5_INCLUDE="${H5_INCLUDE}" \

                -e LDFLAGS="${LDFLAGS}" \

                nanopolish

# Developer Notes

## Updating Bioconda on tagged releases

The following is a quick step-by-step checklist on updating the bioconda release for nanopolish, to be done after each tagged release, and is a condensed/updated version of [these slides](https://monashbioinformaticsplatform.github.io/bioconda-tutorial/#/) by Andrew Perry.

1. On Github, fork `https://github.com/bioconda/bioconda-recipes` to `https://github.com/{USER}/bioconda-recipes` and clone the latter repository to a local directory; `cd` into the cloned directory.

2. Check out a new branch via `git branch nanopolish-bioconda-bump && git checkout nanopolish-bioconda-bump`.

3. Update the `bioconda-recipes/recipes/nanopolish/meta.yaml` file by editing the version tag and the SHA hash; the SHA256 hash can be obtained by running `sha256sum nanopolish-v{$VERSION}.tar.gz` on the command line (where `{VERSION}` is the new, updated version tag); commit the changes to the `meta.yaml` file via, e.g., `git commit -a -m 'bump nanopolish to version {VERSION}'`.

4. Push the changes to your forked repo via `git push origin nanopolish-bioconda-bump`; then, make a pull request to merge the updates into the master branch of the upstream `bioconda-recipes` repository.

5. If all goes well, the automated TravisCI tests on the upstream repository will pass and an owner will merge the changes.

6. Otherwise, if further edits are requested or if the TravisCI tests fail, make further commits to the local cloned repository and push to the forked repository on Github; the changes should automatically appear in the pull request and will trigger an automated TravisCI check.

EIGEN ?= install

HTS ?= install

HDF5_VERSION ?= 1.10.4

HDF5_VERSION ?= 1.8.14

EIGEN_VERSION ?= 3.2.5

# Check operating system, OSX doesn't have -lrt

# Build libhts

#

htslib/libhts.a:

	cd htslib && make || exit 255

	cd htslib && make htslib_default_libs="-lz -lm -lbz2" || exit 255

#

# If this library is a dependency the user wants HDF5 to be downloaded and built.

## Release notes

* 0.11.1: `nanopolish polya` now supports SQK-RNA-002 kits with automatic backwards-compatibility with SQK-RNA-001

* 0.11.0: support for multi-fast5 files. `nanopolish methyltrain` now subsamples input data, improving speed and memory usage

* 0.10.2: added new program `nanopolish polya` to estimate the length of poly-A tails on direct RNA reads (by @paultsw)

Now, we use nanopolish to compute the consensus sequence (the genome is polished in 50kb blocks and there will be one output file per block). We'll run this in parallel:

```

python nanopolish_makerange.py draft.fa | parallel --results nanopolish.results -P 8 \

python3 nanopolish_makerange.py draft.fa | parallel --results nanopolish.results -P 8 \

    nanopolish variants --consensus -o polished.{1}.vcf -w {1} -r reads.fa -b reads.sorted.bam -g draft.fa -t 4 --min-candidate-frequency 0.1

```

master_doc = 'index'

# General information about the project.

project = u'Nanopolish'

copyright = u'2017, Simpson Lab'

author = u'Simpson Lab'

project = 'Nanopolish'

copyright = '2017, Simpson Lab'

author = 'Simpson Lab'

# The version info for the project you're documenting, acts as replacement for

# |version| and |release|, also used in various other places throughout the

# built documents.

#

# The short X.Y version.

version = u'0.8.4'

version = '0.8.4'

# The full version, including alpha/beta/rc tags.

release = u'0.8.4'

release = '0.8.4'

# The language for content autogenerated by Sphinx. Refer to documentation

# for a list of supported languages.

# (source start file, target name, title,

#  author, documentclass [howto, manual, or own class]).

latex_documents = [

    (master_doc, 'Nanopolish.tex', u'Nanopolish Documentation',

     u'Simpson Lab', 'manual'),

    (master_doc, 'Nanopolish.tex', 'Nanopolish Documentation',

     'Simpson Lab', 'manual'),

]

# One entry per manual page. List of tuples

# (source start file, name, description, authors, manual section).

man_pages = [

    (master_doc, 'nanopolish', u'Nanopolish Documentation',

    (master_doc, 'nanopolish', 'Nanopolish Documentation',

     [author], 1)

]

# (source start file, target name, title, author,

#  dir menu entry, description, category)

texinfo_documents = [

    (master_doc, 'Nanopolish', u'Nanopolish Documentation',

    (master_doc, 'Nanopolish', 'Nanopolish Documentation',

     author, 'Nanopolish', 'One line description of project.',

     'Miscellaneous'),

]