update midas pinnings to match docs

[rpetit3]

Updating the pinnings to match the docs: https://github.com/snayfach/MIDAS/blob/master/docs/install.md

I'm doing testing with build 6 docker container and its not liking samtools v1.12

---

Please read the guidelines for Bioconda recipes before opening a pull request (PR).

• If this PR adds or updates a recipe, use "Add" or "Update" appropriately as the first word in its title.
• New recipes not directly relevant to the biological sciences need to be submitted to the conda-forge channel instead of Bioconda.
• PRs require reviews prior to being merged. Once your PR is passing tests and ready to be merged, please issue the @BiocondaBot please add label command.
• Please post questions on Gitter or ping @bioconda/core in a comment.

Please use the following BiocondaBot commands:

Everyone has access to the following BiocondaBot commands, which can be given in a comment:

@BiocondaBot please update	Merge the master branch into a PR.
@BiocondaBot please add label	Add the please review & merge label.
@BiocondaBot please fetch artifacts	Post links to CI-built packages/containers. You can use this to test packages locally.

For members of the Bioconda project, the following command is also available:

@BiocondaBot please merge

Upload built packages/containers and merge a PR. Someone must approve a PR first! This reduces CI build time by reusing built artifacts.

Also, the bot watches for comments from non-members that include @bioconda/<team> and will automatically re-post them to notify the addressed <team>.

[rpetit3]

@BiocondaBot please fetch artifacts

[rpetit3]

@BiocondaBot please fetch artifacts

[BiocondaBot]

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

Arch	Package	Zip File
noarch	midas-1.3.2-pyh7cba7a3_7.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
midas	1.3.2--pyh7cba7a3_7	show gzip -dc LinuxArtifacts/images/midas:1.3.2--pyh7cba7a3_7.tar.gz | docker load

[rpetit3]

@BiocondaBot please fetch artifacts

[BiocondaBot]

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

Arch	Package	Zip File
noarch	midas-1.3.2-pyh7cba7a3_7.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
midas	1.3.2--pyh7cba7a3_7	show gzip -dc LinuxArtifacts/images/midas:1.3.2--pyh7cba7a3_7.tar.gz | docker load

[rpetit3]

@BiocondaBot please fetch artifacts

[BiocondaBot]

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

Arch	Package	Zip File
noarch	midas-1.3.2-pyh7cba7a3_7.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
midas	1.3.2--pyh7cba7a3_7	show gzip -dc LinuxArtifacts/images/midas:1.3.2--pyh7cba7a3_7.tar.gz | docker load

[rpetit3]

@BiocondaBot please fetch artifacts

[BiocondaBot]

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

Arch	Package	Zip File
noarch	midas-1.3.2-pyh7cba7a3_7.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
midas	1.3.2--pyh7cba7a3_7	show gzip -dc LinuxArtifacts/images/midas:1.3.2--pyh7cba7a3_7.tar.gz | docker load

[rpetit3]

I think its better now. On build 6 I was getting this error:

Error: could not execute samtools binary: samtools
(exited with error code 1)
To solve this issue, follow these steps:
  1) Download samtools v1.4: https://github.com/samtools/samtools/releases/download/1.4/samtools-1.4.tar.bz2
  2) Unpack and compile the software on your system
  3) Copy the new samtools binary to:

With the updated patch file It executes now:

MIDAS: Metagenomic Intra-species Diversity Analysis System
version 1.3.0; github.com/snayfach/MIDAS
Copyright (C) 2015-2016 Stephen Nayfach
Freely distributed under the GNU General Public License (GPLv3)

===========Parameters===========
Command: /usr/local/bin/run_midas.py species results -1 SRR2838702_R1.fastq.gz -2 SRR2838702_R2.fastq.gz -d midas/midas/ -t 4
Script: run_midas.py species
Database: midas/midas/
Output directory: results
Input reads (1st mate): SRR2838702_R1.fastq.gz
Input reads (2nd mate): SRR2838702_R2.fastq.gz
Remove temporary files: False
Word size for database search: 28
Minimum mapping alignment coverage: 0.75
Number of reads to use from input: use all
Number of threads for database search: 4
================================

Aligning reads to marker-genes database
  0.04 minutes
  0.77 Gb maximum memory

Classifying reads
  total alignments: 2
  uniquely mapped reads: 0
  ambiguously mapped reads: 0
  0.0 minutes
  0.78 Gb maximum memory

Estimating species abundance
  total marker-gene coverage: 0.0
  0.0 minutes
  0.78 Gb maximum memory

[rpetit3]

@BiocondaBot please add label

[rpetit3]

@BiocondaBot please merge

[BiocondaBot]

I will attempt to upload artifacts and merge this PR. This may take some time, please have patience.