wip readme; fix dockerfile.perl

Dockerfile.perl

@@ -9,7 +9,7 @@
 # needed for minimal installs for Perl to compile
 RUN apt install -y unminimize && yes | unminimize
 
-COPY perl /bystro/install
+COPY perl /bystro/perl
 COPY go /bystro/go
 COPY install /bystro/install
 
@@ -20,4 +20,4 @@
 RUN cd /bystro && ./install-apt.sh
 
 # Ensure .profile gets sourced when the container starts
-CMD ["/bin/bash", "-l"]
+CMD ["/bin/bash", "-c", "source ~/.profile && exec bash"]

install/install-perlbrew-linux.sh

@@ -73,10 +73,10 @@ if ! perlbrew list | grep -q "$VERSION"; then
   nCores=$(getconf _NPROCESSORS_ONLN)
   if [[ "$NOTEST" -eq 0 ]]; then
     echo "Installing Perl $VERSION with $nCores cores (running tests)"
-    perlbrew install "$VERSION" -j "$nCores"
+    perlbrew install "$VERSION" -n -j "$nCores"
   else
     echo "Installing Perl $VERSION with $nCores cores (skipping tests)"
-    perlbrew install "$VERSION" -j "$nCores" -n
+    perlbrew install "$VERSION" -n -j "$nCores" -n
   fi
 else
   echo "Perl version $VERSION is already installed."

perl/README.md

@@ -1,41 +1,86 @@
-# Bystro Annotator Perl package
+# Bystro Annotator Package
 
-## Installing Bystro using docker
+## Installing Bystro Annotator using Docker
 
-To build a docker image using the `Dockerfile`, run the following:
+To build a Docker image using the `Dockerfile`, run the following:
 
 ```bash
-cd ../ && docker build -t bystro-perl -f Dockerfile.perl .
+cd ../ && docker build -t bystro-annotator -f Dockerfile.perl .
 ```
 
-## Installing Bystro using `cpam`
+## Installing Bystro Annotator Bare Metal / Locally
 
-The instructions for installing Bystro locally uses [`cpanm`](https://metacpan.org/pod/App::cpanminus).
+The instructions for installing Bystro locally use [`cpm`](https://metacpan.org/pod/App::cpanminus).
 
-Assuming that you've cloned the repository and are working on it locally, then the dependencies can mostly be installed with cpanm.
+To install `cpm`, run the following:
+
+- If using the system Perl:
+
+  ```bash
+  curl -fsSL https://raw.githubusercontent.com/skaji/cpm/main/cpm | sudo perl - install -g App::cpm
+  ```
+
+- If using local Perl through [perlbrew](https://perlbrew.pl) or [plenv](https://github.com/tokuhirom/plenv), or system Perl but with [local::lib](https://srcc.stanford.edu/farmshare/software-perllocallib) to ensure that libraries are installed locally (thus not requiring `sudo privileges`):
+
+  ```bash
+  curl -fsSL https://raw.githubusercontent.com/skaji/cpm/main/cpm | perl - install -g App::cpm
+  ```
+
+Assuming that you've cloned the repository and are working on it locally, then the dependencies can mostly be installed with cpm.
 But there are a few one-off dependencies that require a slightly modified approach.
 
 One-off dependencies can be installed as follows:
 
 ```bash
-cpanm --quiet https://github.com/bystrogenomics/msgpack-perl.git
-cpanm --quiet --notest MouseX::Getopt
-git clone --depth 1 --recurse-submodules https://github.com/salortiz/LMDB_File.git \
-  && cd LMDB_File \
-  && cpanm --quiet . \
-  && cd .. \
-  && rm -rf LMDB_File
-# 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>
-cpanm --quiet DBD::MariaDB@1.23
+cpm install -g --test https://github.com/bystrogenomics/msgpack-perl.git
+
+ALIEN_INSTALL_TYPE=share cpm install -g --test Alien::LMDB
+cpm install -g --test LMDB_File
+cpm install -g MouseX::Getopt # fails due to differences from expected output; unimportant
 ```
 
-The remaining dependencies are installed like this:
+- Please note, that if you are using Perl > 5.36.0, you will need to manually install LMDB_File 0.14, which will require `make`
+
+  ```bash
+  ALIEN_INSTALL_TYPE=share cpm install -g --test Alien::LMDB
+  git clone --depth 1 --recurse-submodules https://github.com/salortiz/LMDB_File.git \
+    && cd LMDB_File \
+    && git checkout 34acb71d7d86575fe7abb3f7ad95e8653019b282 \
+    && perl Makefile.PL && make distmeta \
+    && ln -s MYMETA.json META.json && ln -s MYMETA.yml META.yml \
+    && cpm install --show-build-log-on-failure -g . \
+    && cd ..
+  ```
+
+- Alternatively you can use [cpanm](https://metacpan.org/dist/App-cpanminus/view/bin/cpanm) to install the LMDB_File 0.14 dependencies:
+
+  ```bash
+    ALIEN_INSTALL_TYPE=share cpm install -g --test Alien::LMDB
+    git clone --depth 1 --recurse-submodules https://github.com/salortiz/LMDB_File.git \
+      && cd LMDB_File \
+      && cpanm . \
+      && cd .. \
+      && rm -rf LMDB_File
+  ```
+
+One of the dependencies, DBD::MariaDB, requires mysql_config to be installed. From DBD::MariaDB documentation:
 
-```bash
-cpanm --installdeps .
 ```
+MariaDB/MySQL
+You need not install the actual MariaDB or MySQL database server, the client files and the development files are sufficient. They are distributed either in Connector/C package or as part of server package. You need at least MySQL version 4.1.8.
+
+For example, Fedora, RedHat, CentOS Linux distribution comes with RPM files (using YUM) mariadb-devel, mariadb-embedded-devel, mysql-devel or mysql-embedded-devel (use yum search to find exact package names). Debian and Ubuntu comes with DEB packages libmariadb-dev, libmariadbclient-dev, libmariadbd-dev, libmysqlclient-dev or libmysqld-dev (use apt-cache search to find exact package names).
+
+In some cases MariaDB or MySQL libraries depends on external libpcre, libaio, libnuma, libjemalloc or libwrap libraries. If it is that case, they needs to be installed before MariaDB/MySQL libraries.
+
+These are sufficient, if the MariaDB/MySQL server is located on a foreign machine. You may also create client files by compiling from the MariaDB/MySQL source distribution and using
+```
+
+We provide the commands to install the dependencies for Ubuntu 22.04 LTS and Amazon Linux 2023, see `../install/install-apt-deps.sh` for Debian based systems like Ubuntu and `../install/install-rpm-deps.sh` for Centos/RedHat based systems like Amazon Linux 2023.
+
+Once the dependencies are installed, you can install the remaining dependencies with `cpm`:
+
+````
 
 After installing dependencies, use `prove -lr t` to run tests.
 
@@ -45,18 +90,21 @@ Bystro uses [`Dist::Zilla`](https://github.com/rjbs/dist-zilla) for packaging an
 This approach requires installing `Dist::Zilla` and author dependencies and one off-dependencies described in the above.
 
 ```bash
+# Install cpm
+curl -fsSL https://raw.githubusercontent.com/skaji/cpm/main/cpm | perl - install -g App::cpm
+
 # Install Dist::Zilla and Archive::Tar::Wrapper (to slightly speed up building)
-cpanm --quiet Dist::Zilla Archive::Tar::Wrapper
+cpm install -g Dist::Zilla Archive::Tar::Wrapper
 
 # Install build dependencies
-dzil authordeps --missing | cpanm --quiet
+dzil authordeps --missing | cpanm
 
 # Install Bystro dependencies
-dzil listdeps --missing | cpanm --quiet
+dzil authordeps --missing | cpanm
 
 # Install Bystro
 dzil install
-```
+````
 
 ## Install Bystro using `cpm`
 

perl/cpanfile

@@ -11,6 +11,7 @@ requires "DBI" => "0";
 requires "DDP" => "0";
 requires "Data::MessagePack" => "0";
 requires "Digest::MD5" => "0";
+requires "Fcntl" => "0";
 requires "File::Basename" => "0";
 requires "File::Glob" => "0";
 requires "File::Which" => "0";
@@ -39,6 +40,7 @@ requires "Pod::Usage" => "0";
 requires "Scalar::Util" => "0";
 requires "String::Strip" => "0";
 requires "Sys::CpuAffinity" => "0";
+requires "Time::HiRes" => "0";
 requires "Time::localtime" => "0";
 requires "Try::Tiny" => "0";
 requires "Type::Params" => "0";
@@ -54,9 +56,13 @@ on 'test' => sub {
   requires "Exporter" => "0";
   requires "ExtUtils::MakeMaker" => "0";
   requires "File::Spec" => "0";
+  requires "File::Temp" => "0";
+  requires "IO::Compress::Gzip" => "0";
+  requires "IO::Uncompress::Gunzip" => "0";
   requires "Test::Exception" => "0";
   requires "Test::More" => "0";
   requires "Types::Common::String" => "0";
+  requires "YAML::Tiny" => "0";
 };
 
 on 'test' => sub {