samtools stats: remove plot_bamstats call #2579
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will work after bioconda/bioconda-recipes#17239 this is merged advantage: no additional mulled environment needed
bernt-matthias
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Is the additional mulled env problematic? I think bioconda will not like it. There was recently a discussion about adding R to Picard and this was shut down. bioconda/bioconda-recipes#3859 What you can do is create a samtools-full packages or similar, but then again you have an additional environment. |
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No real problem, the extra env just takes more memory which is not really necessary. Interesting discussion. I'm pro adding the extra dependency to the package. Lets see what the community thinks. After finding out that multiqc can plot the stats I kind of regret that I added the plot_bamstats call... we might as well remove it .. it would not remove any functionality from Galaxy. |
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Thank remove it :)
If you mean storage here, think about it the other way, everyone that just needs samtools, including all our other tools that include samtools, will get now R and gnuplot as well - in their mulled-env. |
Sugest to the user to use MultiQC instead.. which is much better.
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bernt-matthias
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Would it be OK to keep the version. For me it would be fine if the change goes to the TS with the next mayor improvement of the tools. |
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Not sure how? Do you mean not merging this PR, or merge and kill travis to not upload the recipes? |
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Ahh .. lets just bump :) .. Maybe it would be an option not to upload to the TS if the version is already present in the TS anyway? |
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Can you bump the version ? I don't see the point of holding back releases ? The smaller the release the better IMO. |
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sure. done |
To get rid of the gnuplot and perl dependency
advantage: no additional mulled environment needed
FOR CONTRIBUTOR: