can't install

[dosshra]

Hi
using the "gem install" command I get the following error:

Fetching bio-polyploid-tools-1.2.1.gem
Fetching systemu-2.6.5.gem
Fetching descriptive_statistics-2.5.1.gem
Fetching bio-2.0.5.gem
Fetching bio-samtools-2.6.2.gem
Fetching bio-svgenes-0.4.1.gem
Successfully installed systemu-2.6.5
Successfully installed descriptive_statistics-2.5.1
Successfully installed bio-svgenes-0.4.1
Successfully installed bio-2.0.5
Building native extensions. This could take a while...
ERROR: Error installing bio-polyploid-tools:
ERROR: Failed to build gem native extension.

current directory: /var/lib/gems/3.0.0/gems/bio-samtools-2.6.2/ext
/usr/bin/ruby3.0 mkrf_conf.rb

current directory: /var/lib/gems/3.0.0/gems/bio-samtools-2.6.2/ext
/usr/bin/ruby3.0 -I/usr/lib/ruby/vendor_ruby -rrubygems /usr/share/rubygems-integration/all/gems/rake-13.0.6/exe/rake RUBYARCHDIR=/var/lib/gems/3.0.0/extensions/x86_64-linux/3.0.0/bio-samtools-2.6.2 RUBYLIBDIR=/var/lib/gems/3.0.0/extensions/x86_64-linux/3.0.0/bio-samtools-2.6.2
rake aborted!
Errno::ENOENT: No such file or directory @ rb_sysopen - https://github.com/samtools/samtools/releases/download/1.6/samtools-1.6.tar.bz2
/var/lib/gems/3.0.0/gems/bio-samtools-2.6.2/ext/Rakefile:11:in initialize' /var/lib/gems/3.0.0/gems/bio-samtools-2.6.2/ext/Rakefile:11:in open'
/var/lib/gems/3.0.0/gems/bio-samtools-2.6.2/ext/Rakefile:11:in block in <top (required)>' /usr/share/rubygems-integration/all/gems/rake-13.0.6/exe/rake:27:in

'
Tasks: TOP => default => download
(See full trace by running task with --trace)

rake failed, exit code 1

Gem files will remain installed in /var/lib/gems/3.0.0/gems/bio-samtools-2.6.2 for inspection.
Results logged to /var/lib/gems/3.0.0/extensions/x86_64-linux/3.0.0/bio-samtools-2.6.2/gem_make.out

Thank you

[colindaven]

Using a docker approach worked fine for me. Most of the code is getting the (old and end of life) ruby 2.5.0 which the tool was tested on.

## ADD an ubuntu image up here 

SHELL [ "/bin/bash", "--login", "-c" ]

# Get packages - likely I don't need all of these but the dependencies are critical-  mafft exonerate primer3 
RUN apt-get update && apt-get -y --no-install-recommends install apt-utils libz-dev make g++ libreadline6-dev libssl-dev libreadline-dev curl git build-essential libyaml-dev libpq-dev libffi-dev openbox openssl zlib1g-dev autoconf automake libtool bzip2 bison sqlite patch gcc wget libgmpxx4ldbl gawk gawk-doc libgmp10-doc libmpfr-dev sqlite3-doc libsqlite3-dev pkg-config mafft exonerate primer3 libbz2-dev liblzma-dev ncbi-blast+ gnupg2 libssl-dev libreadline-dev sqlite3 libxml2-dev libxslt1-dev libcurl4-openssl-dev libgmp3-dev libgdbm-dev libncurses5-dev tree gzip libfile-mimeinfo-perl

# Check out ruby-build and install
RUN git clone https://github.com/sstephenson/ruby-build.git /usr/local/ruby-build
RUN /usr/local/ruby-build/install.sh

# Install the version of Ruby we want and add to the path
RUN ruby-build 2.5.0 /usr/local/ruby-2.5.0
ENV PATH="/usr/local/ruby-2.5.0/bin:${PATH}"

RUN echo "$(ruby --version)"

# install polymarker
RUN gem install bio-polyploid-tools

[colindaven]

Oh - by the way, its a ruby version problem. If I use the old ruby-2.5.0 as I've written above, the container works fine. If I use the current most modern version3.3.4in the same docker pipeline, then it fails with the error you had:

Errno::ENOENT: No such file or directory @ rb_sysopen - https://github.com/samtools/samtools/releases/download/1.6/samtools-1.6.tar.bz2

[dosshra]

HI
Thank you for the response. I was able to install the software on a different machine with no problem.