pin tabix version in snippy

[rpetit3]

related to #46114

the pinned vcflib version does not owrk with newer versions of tabixxp

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Add a run_exports section like this:

build:
  run_exports:
    - ...

with ... being one of:

Case	run_exports statement
semantic versioning	{{ pin_subpackage("myrecipe", max_pin="x") }}
semantic versioning (0.x.x)	{{ pin_subpackage("myrecipe", max_pin="x.x") }}
known breakage in minor versions	{{ pin_subpackage("myrecipe", max_pin="x.x") }} (in such a case, please add a note that shortly mentions your evidence for that)
known breakage in patch versions	{{ pin_subpackage("myrecipe", max_pin="x.x.x") }} (in such a case, please add a note that shortly mentions your evidence for that)
calendar versioning	{{ pin_subpackage("myrecipe", max_pin=None) }}

while replacing "myrecipe" with either name if a name|lower variable is defined in your recipe or with the lowercase name of the package in quotes.

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[rpetit3]

@BiocondaBot please fetch artifacts

[BiocondaBot]

Azure

Package(s) built on Azure are ready for inspection:

Arch	Package	Zip File
noarch	snippy-4.6.0-hdfd78af_4.tar.bz2	LinuxArtifacts

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You may also use conda to install these after downloading and extracting the appropriate zip file. From the LinuxArtifacts or OSXArtifacts directories:

conda install -c ./packages <package name>

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Docker image(s) built (images for Azure are in the LinuxArtifacts zip file above):

Package	Tag	Install with docker
snippy	4.6.0--hdfd78af_4	show gzip -dc LinuxArtifacts/images/snippy:4.6.0--hdfd78af_4.tar.gz | docker load

[rpetit3]

Testing on my end

Current build hdfd78af_3 isntalled tabixpp 1.1.2 hd68fcf3_1

mamba create -n snippy-test -c conda-forge -c bioconda snippy
mamba activate snippy
vcfuniq
vcfuniq: error while loading shared libraries: libtabixpp.so.0: cannot open shared object file: No such file or directory

With updated recipe and artifacts

mamba create -n snippy-artifacts -c conda-forge -c bioconda \
    perl \
    'perl-bioperl>=1.7.2' \
    'bwa>=0.7.17' \
    'samtools>=1.10' \
    'bcftools>=1.10' \
    'bedtools>=2.28.0' \
    'parallel>=20170422' \
    'freebayes>=1.3.1' \
    'vcflib>=1.0.0_rc3,<=1.0.2' \
    'tabixpp=1.1.0' \
    'snpeff>=4.3,<=5.0' \
    'vt>=0.5772' \
    'snp-sites>=2.4' \
    'any2fasta>=0.4' \
    'samclip>=0.4' \
    'seqtk>=1.3' \
    'minimap2>=2.17' \
    'openjdk>=11'
mamba activate snippy-artifacts
wget -O LinuxArtifacts.zip https://artprodsu6weu.artifacts.visualstudio.com/A27bcc0f9-b22c-4418-83d8-514809b37fb2/25074ded-3133-43ca-af80-895ab87b53cb/_apis/artifact/cGlwZWxpbmVhcnRpZmFjdDovL2Jpb2NvbmRhL3Byb2plY3RJZC8yNTA3NGRlZC0zMTMzLTQzY2EtYWY4MC04OTVhYjg3YjUzY2IvYnVpbGRJZC81MzQzNi9hcnRpZmFjdE5hbWUvTGludXhBcnRpZmFjdHM1/content?format=zip
unzip LinuxArtifacts.zip
conda install LinuxArtifacts/packages/noarch/snippy-4.6.0-hdfd78af_4.tar.bz2
vcfuniq --help


Usage: vcfuniq <vcf file>

List unique genotypes.  Like GNU uniq, but for VCF records.  Remove
records which have the same positon, ref, and alt as the previous
record.

Type: filter

I think we are good now