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update installation and packaging documentation #311

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update installation and packaging documentation #311

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6cee629
Clarify installation
Oct 21, 2023
fd8ae3f
Update README.md
Oct 21, 2023
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74 changes: 42 additions & 32 deletions perl/README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@ To build a docker image using the `Dockerfile`, run the following:
docker build --tag bystro-cli .
```

## Installing Bystro using `cpam`
## Installing Bystro using `cpanm`

The instructions for installing Bystro locally uses [`cpanm`](https://metacpan.org/pod/App::cpanminus).

Expand All @@ -19,16 +19,23 @@ But there are a few one-off dependencies that require a slightly modified approa
One-off dependencies can be installed as follows:

```bash
# install msgpack fork
cpanm --quiet https://github.com/bystrogenomics/msgpack-perl.git

# install MouseX::Getopt despite some tests failing
cpanm --quiet --notest MouseX::Getopt

# install LMDB_File that comes with latest LMDB
git clone --depth 1 --recurse-submodules https://github.com/salortiz/LMDB_File.git \
&& cd LMDB_File \
&& cpanm --quiet . \
&& cd .. \
&& rm -rf LMDB_File

# install mysql driver
# NOTE: you will need mysql_config to install this
# ubuntu 22.04 LTS => sudo apt install -y libmariadb-dev libmariadb-dev-compat
# amazon 2023 => sudo yum install -y <mariadb105>
# amazon 2023 => sudo yum install -y mariadb105-devel.x86_64
cpanm --quiet DBD::mysql@4.051
```

Expand All @@ -38,59 +45,62 @@ The remaining dependencies are installed like this:
cpanm --installdeps .
```

After installing dependencies, use `prove -lr t` to run tests.

## Installing Bystro locally using dzil

Bystro uses [`Dist::Zilla`](https://github.com/rjbs/dist-zilla) for packaging and is configured with `dist.ini`.
This approach requires installing `Dist::Zilla` and author dependencies and one off-dependencies described in the above.

```bash
# Install Dist::Zilla and Archive::Tar::Wrapper (to slightly speed up building)
cpanm --quiet Dist::Zilla Archive::Tar::Wrapper

# Install build dependencies
dzil authordeps --missing | cpanm --quiet

# Install Bystro dependencies
dzil listdeps --missing | cpanm --quiet

# Install Bystro
dzil install
```

## Install Bystro using `cpm`

Install [cpm](https://metacpan.org/pod/App::cpm) with `curl -fsSL https://raw.githubusercontent.com/skaji/cpm/main/cpm | perl - install -g App::cpm`.

```bash
# install msgpack fork
cpm https://github.com/bystrogenomics/msgpack-perl.git
cpm install -g https://github.com/bystrogenomics/msgpack-perl.git
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we use cpm here and cpanm above; could we go to cpm throughout? I have a change I can make the corresponding change to the perlbrew script

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The problem with using cpm throughout is that cpanm is needed for installing LMDB_File - at least I couldn't find a way of using it. If your concern is that it is confusing to have two sections - one for cpamn and one for cpm - then I suggest consolidation of the two approaches with the acknowledgement that both tools are needed.


# install MouseX::Getopt despite some tests failing
cpm --no-test MouseX::Getopt
cpm install -g --no-test MouseX::Getopt

# install LMDB_File that comes with latest LMDB
# NOTE: you will need mysql_config to install this
# ubuntu 22.04 LTS => sudo apt install -y libmariadb-dev libmariadb-dev-compat
# amazon 2023 => sudo yum install -y <mariadb105>
git clone --depth 1 --recurse-submodules https://github.com/salortiz/LMDB_File.git \
&& cd LMDB_File \
&& cpanm . \
&& cd .. \
&& rm -rf LMDB_File

# install mysql driver
cpm DBD::mysql@4.051
# NOTE: you will need mysql_config to install this
# ubuntu 22.04 LTS => sudo apt install -y libmariadb-dev libmariadb-dev-compat
# amazon 2023 => sudo yum install -y mariadb105-devel.x86_64
cpm install -g DBD::mysql@4.051

# clone bystro and change into perl package
git clone git@github.com:bystrogenomics/bystro.git && cd bystro/perl

# install dependencies
# install dependencies (uses cpanfile)
cpm install -g --with-develop
```

After installing dependencies, use `prove -lr t` to run tests.

## Installing development tools

These are tools needed for packaging and releasing Bystro's Perl package, which are not needed for normal testing or development.

Bystro uses [`Dist::Zilla`](https://github.com/rjbs/dist-zilla) for packaging and is configured with `dist.ini`.
This approach requires installing `Dist::Zilla` and author dependencies and one off-dependencies described in the above.

```bash
# Install Dist::Zilla and Archive::Tar::Wrapper (to slightly speed up building)
cpanm --quiet Dist::Zilla Archive::Tar::Wrapper
# - or -
cpm install -g Dist::Zilla Archive::Tar::Wrapper

# Install build dependencies
dzil authordeps --missing | cpanm --quiet
# - or -
cpm install -g $(dzil authordeps --missing)

# Install Bystro Package
dzil install

# Install dzil build dependencies
RUN cpm install -g --show-build-log-on-failure $(dzil authordeps --missing)
# Test Bystro Package
dzil test --all
```

## Coding style and tidying
Expand Down