More bioperl modules need packaging

[Andreas Tille <andreas@an3as.eu>]

Hi Carnë,

when beeing here at BioHackathon I had some discussion about packaging
ensembl libs.  I'm not really sure what might be a good package to start
but I picked libensembl-bio-db-hts-perl[1].  You see that I prefixed the
upstream name by libensembl and postfixed by -perl as per Perl modules
policy.  Feel free to comment on that naming scheme.

Unfortunately I was not able to tell the configure step where to find
htslib.  I'd assume it should be detected automatically but since it
is not I tried the following three methods - all with no success:

# dh_auto_configure -- --prefix=/usr
# dh_auto_configure -- --htslib-includedir=/usr/include
HTSLIB_DIR=/usr/include dh_auto_configure
        perl Build.PL --installdirs vendor --config "optimize=-g -O2 -fdebug-prefix-map=/build/libensembl-bio-db-hts-perl-98+git20190710.83c9327=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" --config "ld=x86_64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/build/libensembl-bio-db-hts-perl-98+git20190710.83c9327=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro"
HTSLIB_DIR=/usr/include environment variable does not contain expected files

This module requires HTSlib (http://htslib.org/)
Install it if you have not done so already.

This script will attempt to locate HTSlib by looking for htslib/hts.h
and libhts.a / libhts.so in:

  1. --htslib-includedir and --htslib-libdir command line arguments
  2. --htslib command line argument
  3. HTSLIB_DIR environment variable
  4. --prefix command line argument (which also sets installation location)
  5. Alien::HTSlib dependency resolver
  6. pkg-config (extra directories can be set in PKG_CONFIG_PATH environment variable)
  7. common library locations: /usr /usr/local, /usr/share, /opt/local

If none of the above succeeds but htslib is registered with pkg-config, the script
will try using pkg-config paths (via ExtUtils::PkgConfig) without checking if header
and library files exist.


Any hint how to fix this?

Kind regards

     Andreas.


[1] https://salsa.debian.org/med-team/libensembl-bio-db-hts-perl
    https://github.com/Ensembl/Bio-DB-HTS

-- 
http://fam-tille.de