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Following the installation of Anvio (#23) we can now run it by activating the mamba environment `anvio-8`.
Lets create a new directory for the anvio run that we will use as the working dir.
```
m…
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## Structured standard
After multiple different approaches i am now confident in an approach. To create a set standard, i will redo the scripts so the same analysis and structure is withheld unregard…
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Hi! I'm trying to import the results from ghostkoala to anvio and I'm following your procedure https://merenlab.org/2018/01/17/importing-ghostkoala-annotations/ but when I arrive at this point:
pytho…
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## Anvio-8 (CHECK LAST COMMENT FOR BEST INSTALL)
Anvio is not available as a module on Rackham and has to be manually installed in ones `conda` environment. The steps to install Anvio was gathered fr…
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We want to be able to load the RASTTk annotations to anvio to compare the annotations used in the model to what Michelle got from the pangenome.
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trying to install anvio via ```conda create -n avio anvio``` keeps failing for me due to apparently unresolvable conflicts between different dependencies
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## The need
Diamond can generate a lot of temporary files. The default /tmp can get full on clusters.
## The solution
Add a parameter `--temp` to the command `anvi-pan-genome`, maybe others t…
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## Short description of the problem
Attempting to generate DAG diagrams with `anvi-run-workflow --save-workflow-graph` results in an error due to pulp v2.8.0 which installs with anvi'o v8.
## an…
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The current anvio recipe tries to install the most recent version of samtools. However the anvio webpage explicitely states that anvio will not work with samtools versions other than 1.9.
has this ch…
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First, all reads are merged.
We skip the CO_ and CH_ as they contain all reads for hostplant respectively.
```
ls -1 05-CLEAN-MERGED/* | paste - - | grep -v "CO_" | grep -v "CH_" > doc/all-clean-re…