compara-cloud-dependencies

After installing dependencies for running the protein trees pipeline to google cloud platform, a set of shell scripts were developed. These are those.

These instructions are an amalgamation of the following:

• https://github.com/Ensembl/linuxbrew-automation/blob/master/01-base-libraries.sh
• https://hub.docker.com/r/muffato/ensembl-linuxbrew-basic-dependencies/dockerfile
• https://hub.docker.com/r/muffato/ensembl-linuxbrew-compara-base/dockerfile
• https://hub.docker.com/r/muffato/ensembl-linuxbrew-compara-proteintrees/dockerfile

Steps

1. source envs.sh
2. run shell scripts in order:
   • 1.linuxbrew_basic_dependencies.sh
   • 2.linuxbrew_compara_base.sh
   • 3.linuxbrew_compara_proteintrees.sh

Notes / Known Issues

xz

• xz was failing make check tests when installing through brew install ensembl/cask/basic-dependencies
  • solution was to manually install xz in the correct location: ./configure --prefix=$ENSEMBL_LINUXBREW_DIR/Cellar/xz/5.2.5 && make && make install
  • brew link xz

percona-client

• percona-client install failing: $ENSEMBL_LINUXBREW_DIR/include/sys/types.h:33:9: error: unknown type name '__u_char' typedef __u_char u_char;
  • tried editing formula ($ENSEMBL_LINUXBREW_DIR/Library/Taps/ensembl/homebrew-external/percona-client.rb) to include new CFLAGs: -Du_char="unsigned char"
  • these needed to be included in both the cmake and make commands : not successful
  • solution was to remove dependencies (and hope it doesn't bite later):
    • edit /apps/compara/linuxbrew/Library/Taps/ensembl/homebrew-cask/yml/perl-clibs.yml and remove percona, kent (as it has percona as a dependency)
    • regenerate the cask: bin/create_cask --verbose --config yml/perl-clibs.yml --dir .
    • remove cached files: ~/.cache/Homebrew/downloads/<SHA256>--<dep name>.rb
    • brew install ensembl/cask/perl-clibs again

graphviz / bison

• brew can't install graphviz : compilation error with dep bison
  • exact same issue as this: Re: complain.c:(.text+0x6df): undefined reference to `ostream_printf'
  • looks like either updating to super super new gettext-0.21 release fixes (first try brew install gettext)
  • or downgrade bison to 3.6.4

hcluster

• trouble with hcluster: formula is set to use svn to download v0.5.0
  • brew install svn is breaking down due to krb5 error
  • first try: edit formula to grab a v0.5.1 I found on github: https://github.com/douglasgscofield/hcluster
    • can then update the download strategy in the formula to :using => :git

harfbuzz

• harfbuzz failing to compile:
  • Harfbuzz fails to build on Ubuntu 20.04 (WSL 2) · Issue #20888 · Homebrew/linuxbrew-core · GitHub
  • disabled glib, gobject, introspection

DBD::mysql

• DBD::mysql is a nightmare to install!!
  • in the end, some environment variables (see envs.sh) to set up mysql connection credentials helped
  • needed to set export LD_LIBRARY_PATH=/usr/lib:/usr/lib64:/usr/lib64/mysql so that all the libs were found
  • cpanm DBD::mysql --force had to be used because of testing failures