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ressy
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Sep 11, 2019
ressy
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- Improved icon setup on Mac OS (Compile icon app on MacOS at build time #48).
- Added support for use of reverse primers in locus-matching (Enable support for reverse primers in locus-matching #47).
- Made read count ratio thresholds for PCR stutter and artifact sequence flagging customizable (Configurable threshold for stutter and artifact matching #46).
- Added drag-and-drop usage message when desktop icon is opened directly (Better usage message when desktop icon is opened #44).
- Added load_csv and save_csv functions to centralize loading and saving tabular data (CSV input/output wrapper functions #43).
- Reorganized installer and wrapper scripts (Reorganize installers #38).
- Added support for demo scripts and integration testing in Mac OS (Configure Travis and Demos for Mac OS X Support #32).
No real changes, just incorporating the pull request merges for previous releases.
The pwd behavior looks to be the same between Linux and Mac OS (unlike for readlink) so this should work on both.
We're not developing a bioconductor package
The devel build URL is out of date for osx.
Configure Travis and Demos for Mac OS X Support
Once the R script content is more generalized the other OS wrapper scripts can call this same R script.
Still need to fill in stubs for linux and osx cases.
This variable is available to a running R process even if it didn't exist when R started. This means we can use it for the appropriate per-user library path on a given install and not worry about OS detection.
== for strings, -eq for numbers! This is why it was trying to use the linux installer for osx.
system2 command arguments are given as a character vector, not as separate arguments.
test -d on the directory symlink, not test -f.
Otherwise it will create a symlink inside the target, making a circle.
These functions may be helpful from within an install (e.g. to keep the Desktop icon valid as #24 describes). This also removes the brittle attempts to autodetect paths and instead requires that the wrapper install script be called from the project dir and install() function be given a package source path.
Better usage message when desktop icon is opened
Mention drag-and-drop early in user guide
Configurable threshold for stutter and artifact matching
Add support (off by default to match current behavior) for the ReversePrimer column in the locus_attrs table when calling analyze_seqs as an additional restriction on locus-matching. Either orientation is supported.
Enable support for reverse primers in locus-matching
R's install process skips over directories in exec/, and Mac OS applications are actually directories. Switching to inst/ instead.
Compile icon app on MacOS at build time
I hear devtools can magically install packages from bioconductor. Let's try it. https://bioinformatics.stackexchange.com/a/3375
If devtools is really supplying msa, we don't need Travis to think about it.
Handle Bioconductor packages via devtools
I see errors on some platforms related to [[. Switching to the "test" builtin instead.
Apparently setting variables doesn't work like I expected in the if/else blocks in cmd.exe.
ressy
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Jan 30, 2020
Not sure why this is needed when testing on Travis, but repeating the attempt a few times over gets it working.
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