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Merge pull request #239 from smithlabcode/remove-old-makefiles
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Removing Makefiles from the repo
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@andrewdavidsmith
andrewdavidsmith authored Jul 23, 2024
2 parents 8e82292 + 925ff00 commit 8dc174a
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36 changes: 0 additions & 36 deletions Makefile
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56 changes: 27 additions & 29 deletions README.md
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Expand Up @@ -12,7 +12,7 @@ sequencing (RRBS). These tools focus on overcoming the computing
challenges imposed by the scale of genome-wide DNA methylation data,
which is usually the early parts of data analysis.

## Installing release 1.4.2
## Installing release 1.4.3

The documentation for DNMTools can be found
[here](https://dnmtools.readthedocs.io). But if you want to install
Expand All @@ -23,11 +23,12 @@ all the formatting.
### Required libraries

* A recent compiler. Most users will be building and installing this
software with GCC. We require a compiler that supports C++17, so we
recommend using at least GCC 8 (released in 2018). There are still
many systems that install a very old version of GCC by default, so
if you have problems with building this software, that might be the
first thing to check.
software with GCC. We require a compiler that fully supports C++17,
so we recommend using at least GCC 9 (released in 2019). There are
still many systems that install a very old version of GCC by
default, so if you have problems with building this software, that
might be the first thing to check. The clang LLVM compiler can
also be used with a recent enough version.
* The GNU Scientific Library. It can be installed using apt on Linux
(Ubuntu, Debian), using brew on macOS, or from source available
[here](http://www.gnu.org/software/gsl).
Expand All @@ -41,14 +42,14 @@ repo, it is easiest if all dependencies are available through conda.

### Configuration

* Download [dnmtools-1.4.2.tar.gz](https://github.com/smithlabcode/dnmtools/releases/download/v1.4.2/dnmtools-1.4.2.tar.gz).
* Download [dnmtools-1.4.3.tar.gz](https://github.com/smithlabcode/dnmtools/releases/download/v1.4.3/dnmtools-1.4.3.tar.gz).
* Unpack the archive:
```console
tar -zxvf dnmtools-1.4.2.tar.gz
tar -zxvf dnmtools-1.4.3.tar.gz
```
* Move into the dnmtools directory and create a build directory:
```console
cd dnmtools-1.4.2 && mkdir build && cd build
cd dnmtools-1.4.3 && mkdir build && cd build
```
* Run the configuration script:
```console
Expand Down Expand Up @@ -88,22 +89,23 @@ any arguments and you should see the list of available commands:
```console
dnmtools
```
There is a test suite for `dnmtools` and these test can be performed
as follows:
```console
make check
```
This must be done from the build directory. Note that the tests
performed with `make check` are mostly regression tests that cover
prior issues rather than coverage tests to test all the functionality
of `dnmtools`.

### Using a clone of the repo

Not recommended, but if you want to do it this way, we assume you know
what you are doing. We strongly recommend using DNMTools through the
latest stable release under the releases section on GitHub. Developers
who wish to work on the latest commits, which are unstable, can
compile the source using a `Makefile` left in the root of the source
tree. If HTSLib and other libraries are available system-wide,
compile by running:
```console
make
```
This functionality will probably be removed soon, and if you want to
build the code this way, you should know what you are doing any be
able to make it work yourself.
We strongly recommend using DNMTools through the latest stable release
under the releases section on GitHub or through a package as with
conda/mamba. Developers who wish to work on the latest commits, which
are unstable, can compile the source using `autogen.sh` which just
wraps `autoreconf`.

## Usage

Expand Down Expand Up @@ -137,7 +139,7 @@ docker tag ghcr.io/smithlabcode/dnmtools:latest dnmtools:latest

You can also install the image for a particular vertion by running
```console
docker pull ghcr.io/smithlabcode/dnmtools:v[VERSION NUMBER] #(e.g. v1.4.2)
docker pull ghcr.io/smithlabcode/dnmtools:v[VERSION NUMBER] #(e.g. v1.4.3)
```
Not all versions have corresponding images; you can find available images
[here](https://github.com/smithlabcode/dnmtools/pkgs/container/dnmtools).
Expand Down Expand Up @@ -205,24 +207,20 @@ docker run -v ./:/app -w /app \
dnmtools abismal -v -t 1 -i artifacts/tRex1.idx artifacts/simreads_{1,2}.fq
```


## Contacts and bug reports

Andrew D. Smith
[email protected]

Guilherme de Sena Brandine
[email protected]

## Copyright and License Information

Copyright (C) 2022-2023
Copyright (C) 2022-2024
Andrew D. Smith and Guilherme de Sena Brandine

Authors of DNMTools: Andrew D. Smith and Guilherme de Sena Brandine

Essential contributors: Ben Decato, Meng Zhou, Liz Ji, Terence Li,
Jenny Qu, Qiang Song and Fang Fang
Jenny Qu, Qiang Song, Fang Fang and Masaru Nakajima

This is free software: you can redistribute it and/or modify it under
the terms of the GNU General Public License as published by the Free
Expand Down
50 changes: 22 additions & 28 deletions docs/content/quickstart.md
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Expand Up @@ -50,19 +50,17 @@ would need to be activated when you want to use dnmtools.

### Required libraries

* A recent compiler: most users will be building and installing this
* A recent compiler. Most users will be building and installing this
software with GCC. We require a compiler that fully supports C++17,
so we recommend using at least GCC 8 (released in 2018). There are
so we recommend using at least GCC 9 (released in 2019). There are
still many systems that install a very old version of GCC by
default, so if you have problems with building this software, that
might be the first thing to check. On macOS and Ubuntu/Debian
systems, the brew and apt package managers can get you a recent
compiler easily. Any cluster or high-performance computing
environment should give you access to a recent compiler.
* The GNU Scientific Library: this has always been required. It can be
installed using apt on Linux (Ubuntu, Debian), using brew on macOS,
or from source available [here](http://www.gnu.org/software/gsl).
* The HTSlib library, which can be installed through brew on macOS,
might be the first thing to check. The clang LLVM compiler can
also be used with a recent enough version.
* The GNU Scientific Library. It can be installed using apt on Linux
(Ubuntu, Debian), using brew on macOS, or from source available
[here](http://www.gnu.org/software/gsl).
* The HTSlib library. This can be installed through brew on macOS,
through apt on Linux (Ubuntu, Debian), or from source downloadable
[here](https://github.com/samtools/htslib).
* The Zlib compression library: Most likely you already have this
Expand All @@ -72,14 +70,14 @@ would need to be activated when you want to use dnmtools.

### Configuration

* Download [dnmtools-1.4.2.tar.gz](https://github.com/smithlabcode/dnmtools/releases/download/v1.4.2/dnmtools-1.4.2.tar.gz).
* Download [dnmtools-1.4.3.tar.gz](https://github.com/smithlabcode/dnmtools/releases/download/v1.4.3/dnmtools-1.4.3.tar.gz).
* Unpack the archive:
```console
$ tar -zxvf dnmtools-1.4.2.tar.gz
$ tar -zxvf dnmtools-1.4.3.tar.gz
```
* Move into the dnmtools directory and create a build directory:
```console
$ cd dnmtools-1.4.2
$ cd dnmtools-1.4.3
$ mkdir build && cd build
```
* Run the configuration script:
Expand Down Expand Up @@ -119,25 +117,21 @@ $ export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/path/to/htslib/lib
To test if everything was successful, simply run `dnmtools` without
any arguments and you should see the list of available commands:
```console
$ dnmtools
dnmtools
```
If you want to do more extensive tests, you can run:
There is a test suite for `dnmtools` and these test can be performed
as follows:
```console
$ make check
make check
```
from the directory where you run `make`. This will to several tests of
various commands within `dnmtools`, and might take some time.
This must be done from the build directory. Note that the tests
performed with `make check` are mostly regression tests that cover
prior issues rather than coverage tests to test all the functionality
of `dnmtools`.

## Using a clone of the repo

*This option is deprecated; we are no longer maintaining a Makefile
that is not generated by `./configure`.* Not recommended, but if you
want to do it this way, we assume you know what you are doing. We
strongly recommend using dnmtools through the latest stable release
We strongly recommend using dnmtools through the latest stable release
under the releases section on GitHub. Developers who wish to work on
the latest commits, which are unstable, can compile the source using
the `Makefile` available in the root of the source tree. If HTSLib and
other libraries are available system-wide, compile by running:
```console
$ make
```
the latest commits, which are unstable, can start the process using
the `autogen.sh` script and then using the usual autotools approach.
98 changes: 0 additions & 98 deletions src/Makefile
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