Comments (5)
Hi, the tutorial for the current version of CAMISIM can be found when clicking on CAMISIM 1.3
. There is a new nextflow-based version of CAMISIM in the making and we already updated the wiki accordingly, the nextflow version can only be found on the dev
branch. Feel free to already test that, you will have to do a git checkout dev
first though.
If you want to use the current/published version of CAMISIM, you should refer to the wiki I linked above. Sorry for the confusion.
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@AlphaSquad Is it possible to provide the conda env yml file that has been tested in the unix env?
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The nextflow version is not extensively tested and there is no yaml file available at this moment
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@AlphaSquad I am trying to run the version that you have suggested above. Installing the required tools in unix is kind a challenge. Wondering if you could share the conda env yml file so that I can create the exact conda env in my machince. I am running in unix system.
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This is an environment with which CAMISIM works on our servers (txt
since you cannot upload yml
files to issues): camisim.txt. I cannot guarantee this is the minimal set of software required.
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Related Issues (20)
- Hi,I still cant understand what "adundance" means ………… HOT 1
- should i download all the reference genomes of the species involved in the BIOM file? HOT 1
- some error when i try the command ---- "python metagenome_form_profile.py -p defaults/mini.biom " HOT 1
- Changing temp_directory in config file HOT 4
- Input genomes HOT 3
- ERROR: [MetagenomeSimulationPipeline] 'M' in line 122 HOT 4
- Meaning of community parameters in config file HOT 1
- Is profile-based design with custom genomes possible? HOT 11
- Errors when running from_profile default HOT 8
- How can I simulate reads data when I manually designed an OTU table? HOT 4
- ERROR: [MetagenomeSimulationPipeline] 'utf-8' codec can't decode byte 0x8b in position 1: invalid start byte in line 49? HOT 3
- how to increase the size of the simulated dataset? HOT 1
- No file found for all the reads of the sample in the output HOT 2
- camisim encountered an error when specifying the --hmm_model parameter in pbsim2 HOT 3
- How to map relevant genomes to OTU through scientific names? HOT 11
- Generation from different genome for same specie HOT 4
- Controlling the rate of error HOT 1
- the data type of CAMISIM long read dataset HOT 1
- Confused by the abundance values in the CAMI2 toy datasets HOT 1
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