Moderator: Philipp Bayer

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Philipp Bayer6.5k
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PhilippBayer
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Post-Doc bioinformatics at the University of Western Australia, co-founder openSNP.org

Posts by Philipp Bayer

<prev • 524 results • page 2 of 53 • next >
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Answer: A: Augustus output (GFF file) to Anvi`o
... I've made good experiences with this script: https://github.com/jorvis/biocode/blob/master/gff/convert_augustus_to_gff3.py when downstream software wasn't liking the AUGUSTUS gff3 (you'll have to run `pip install biocode` first) ...
written 4 months ago by Philipp Bayer6.5k
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Answer: A: Bias in GO enrichment analysis for non-model organsim?
... Yes, this is an important point that is often ignored in plant genomics papers! Here's a paper discussing GO database bias, with a bit on the bias imported by unannotated genes, but this is all in human: https://www.nature.com/articles/s41598-018-23395-2 The other problem is that most of your genes ...
written 4 months ago by Philipp Bayer6.5k
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Comment: C: Augustus Installation error
... `conda install boost` could solve this (perhaps then reinstalling augustus) ...
written 4 months ago by Philipp Bayer6.5k
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Comment: C: Augustus Installation error
... Seconding conda, if you don't want conda it's a common error message for which are numerous workarounds on the internet, see for example https://iamphioxus.org/2017/05/08/installing-augustus-with-manual-bamtools-installation/ (I also edited the code in the OP post) ...
written 4 months ago by Philipp Bayer6.5k
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Comment: C: How to get my tool on Homebrew ?
... You make a formula for 1.0 and submit that, later you can submit a pull request for 1.1 with a new version of the same formula ...
written 4 months ago by Philipp Bayer6.5k
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Comment: C: How to get my tool on Homebrew ?
... Maybe both? You can try running brew install --verbose --debug repeat-test which will run through the whole installation without your manual input. brew install --interactive repeat-test won't install the package, but will put you into a sandbox where all of your specified prerequisite ...
written 4 months ago by Philipp Bayer6.5k
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Comment: C: How to get my tool on Homebrew ?
... What happens if you run ./configure --disable-debug --disable-dependency-tracking --disable-silent-rules --prefix=/home/linuxbrew/.linuxbrew/Cellar/repeat-test/1.1 in the --interactive mode? The --interactive mode itself doesn't do much, if you look at the [cookbook](https://docs.brew.sh/For ...
written 4 months ago by Philipp Bayer6.5k
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Comment: C: How to get my tool on Homebrew ?
... how does the full 01.configure file look like? ...
written 4 months ago by Philipp Bayer6.5k
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Comment: C: How to get my tool on Homebrew ?
... Hmmm looking at the entire log, not just the last 15 lines may be more useful ...
written 4 months ago by Philipp Bayer6.5k
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Comment: C: How to get my tool on Homebrew ?
... Have a look at some other formulas - https://github.com/brewsci/homebrew-bio/blob/ea1b171f78eca1a8e2579d385ec6c80db9c09e2b/Formula/das_tool.rb has a few lines where it installs the ggplot2, doMC and data.table R-packages ...
written 4 months ago by Philipp Bayer6.5k

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