Update mlst recipe to include helper scripts

[rpetit3]

This PR adds helper scripts in mlst to the PATH

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[rpetit3]

@BiocondaBot please fetch artifacts

[BiocondaBot]

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

Arch	Package	Zip File
noarch	mlst-2.23.0-hdfd78af_1.tar.bz2	LinuxArtifacts

---

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>

---

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

Package	Tag	Install with docker
mlst	2.23.0--hdfd78af_1	show gzip -dc LinuxArtifacts/images/mlst:2.23.0--hdfd78af_1.tar.gz | docker load

[rpetit3]

Testing

[17:46:56] This is mlst 2.23.0 running on linux with Perl 5.032001
[17:46:56] Checking mlst dependencies:
[17:46:56] Found 'blastn' => /usr/local/bin/blastn
[17:46:56] Found 'any2fasta' => /usr/local/bin/any2fasta
[17:46:57] Found blastn: 2.13.0+ (002013)
[17:46:57] Excluding 3 schemes: abaumannii ecoli vcholerae_2
[17:46:58] Found exact allele match saureus.yqiL-3
[17:46:58] Found exact allele match saureus.pta-4
[17:46:58] Found exact allele match saureus.glpF-1
[17:46:58] Found exact allele match saureus.aroE-3
[17:46:58] Found exact allele match saureus.arcC-3
[17:46:58] Found exact allele match saureus.gmk-1
[17:46:58] Found exact allele match saureus.tpi-4
[17:46:58] Found exact allele match efaecium.gyd-87
[17:46:58] Somehow this tool escaped my normal Australiana based naming system.
[17:46:58] Done.

docker run --rm -u $(id -u):$(id -g) quay.io/biocontainers/mlst:2.23.0--hdfd78af_1 mlst-download_pub_mlst -h
SYNOPSIS
  Download PubMLST schemes
USAGE
  mlst-download_pub_mlst [options] -d OUTDIR
OPTIONS
  -h       Show this help
  -v       Verbose output
  -j CPUS  Parallel download threads [1]
  -x CSV   Ignore these schemes [afumigatus,blastocystis,calbicans,cglabrata,ckrusei,ctropicalis,csinensis,kseptempunctata,sparasitica,tvaginalis]
  -d DIR   Output folder []
  -n       Don't run download commands
END

docker run --rm -v ${PWD}:/data -u $(id -u):$(id -g) quay.io/biocontainers/mlst:2.23.0--hdfd78af_1 mlst-download_pub_mlst -d /data
This is mlst-download_pub_mlst
Found curl - /usr/local/bin/curl
ERROR: Please install 'parallel'

need to add somethings

[rpetit3]

close in favor of #38813