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update midas pinnings to match docs #38566

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Merged
merged 6 commits into from
Dec 28, 2022
Merged

update midas pinnings to match docs #38566

merged 6 commits into from
Dec 28, 2022

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rpetit3
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@rpetit3 rpetit3 commented Dec 27, 2022

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

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rpetit3 commented Dec 27, 2022

@BiocondaBot please fetch artifacts

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rpetit3 commented Dec 27, 2022

@BiocondaBot please fetch artifacts

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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
showgzip -dc LinuxArtifacts/images/midas:1.3.2--pyh7cba7a3_7.tar.gz | docker load

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rpetit3 commented Dec 27, 2022

@BiocondaBot please fetch artifacts

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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
showgzip -dc LinuxArtifacts/images/midas:1.3.2--pyh7cba7a3_7.tar.gz | docker load

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rpetit3 commented Dec 27, 2022

@BiocondaBot please fetch artifacts

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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
showgzip -dc LinuxArtifacts/images/midas:1.3.2--pyh7cba7a3_7.tar.gz | docker load

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rpetit3 commented Dec 28, 2022

@BiocondaBot please fetch artifacts

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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
showgzip -dc LinuxArtifacts/images/midas:1.3.2--pyh7cba7a3_7.tar.gz | docker load

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rpetit3 commented Dec 28, 2022

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

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rpetit3 commented Dec 28, 2022

@BiocondaBot please add label

@BiocondaBot BiocondaBot added the please review & merge set to ask for merge label Dec 28, 2022
@rpetit3 rpetit3 requested a review from npavlovikj December 28, 2022 15:23
@rpetit3 rpetit3 mentioned this pull request Dec 28, 2022
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rpetit3 commented Dec 28, 2022

@BiocondaBot please merge

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

@BiocondaBot BiocondaBot merged commit 0e8214b into master Dec 28, 2022
@BiocondaBot BiocondaBot deleted the rpetit3-patch-midas branch December 28, 2022 16:51
cokelaer pushed a commit to cokelaer/bioconda-recipes that referenced this pull request Apr 28, 2023
@rpetit3 @cokelaer
[ci skip] Merge PR 38566
9f36f64 
Merge PR bioconda#38566, commits were: 
 * remove redundant check
 * another tweak
 * tweak patch
 * update patch to use samtools --help in stead of view
 * fix typo
 * update midas pinnings to match docs
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@matthdsm matthdsm matthdsm approved these changes

@npavlovikj npavlovikj Awaiting requested review from npavlovikj

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