Open mortonjt opened 6 years ago
I am listing external programs I found in the different modules here: I figure native unix tools like "scp", "touch", ... will be there, but we should maybe test their presence, therefore I listed them, too. @tanaes could you double check if these lists are complete / correct?
Anvio: @mortonjt has been working on a unified conda recipe for this tool, so let's defer on that for now.
I don't think it's that important to test for basic *nix tools, is it?
Assemble: quast.py and metaquast.py are in same package
Bin: pileup.sh is in the BBmap recipe maxbin2 is the other one we need. I have had trouble with this one.
Map: bowtie2-build and bowtie2 are both in bowtie2
Mash: waiting for @RNAer to update with SourMash
Report: I think these actually need to be added to the base oecophylla environment, because these are executed in that context?
I feel that there is a lot of code duplication for all those more or less small .yaml and .sh files for the conda installation of the modules plus a lot of places where they can get out of sync:
Could we somehow centralize the knowledge about the modules and generate the necessary .yaml and .sh files?
the versions can be different in different conda env because one pkg requires v2 and another v3?
On Sep 14, 2017, at 9:37 AM, Stefan Janssen notifications@github.com wrote:
I feel that there is a lot of code duplication for all those more or less small .yaml and .sh files for the conda installation of the modules plus a lot of places where they can get out of sync:
conda env prefix: "oecophilla" vs "shotgu" different conda package versions: "hmmer" vs. "hmmer ==3.1." Could we somehow centralize the knowledge about the modules and generate the necessary .yaml and .sh files?
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seqtk does not appear to be installing correctly. If you install following the readthedocs tutorial and then run the test you get:
"/bin/bash: line 8: seqtk: command not found /bin/bash: line 8: seqtk: command not found Error in rule taxonomy_shogun: jobid: 0 output: results/taxonomy/sample_S22282/shogun/sample_S22282.profile.txt log: results/taxonomy/logs/taxonomy_shogun.sample=[sample_S22282].log
RuleException: ..."
Manually installing seqtk and adding it to PATH resolved this issue.