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flexible pipelines for scalable secretome prediction, R package
install('SecretSanta')
Installing SecretSanta
'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet CMD INSTALL \
'/home/anna/anna/Labjournal/SecretSanta' --library='/home/anna/R/x86_64-pc-linux-gnu-library/3.4' --install-tests
Error: Command failed (127)
(internal links) => might improve readability
bring the slow integration test back
update dependencies?
when running the targetp function, when the backend is pointing to targetp v2.0c, the code fails with the message:
flag provided but not defined: -N
Usage of targetp:
...usage statement for targetp...
Error in checkForRemoteErrors(val) :
one node produced an error: 'names' attribute [7] must be the same length as the vector [1]
Is this because SecretSanta will only work with the older version of targetp (v1.1)? I would have just tried that before posting here but I haven't been able to find an old version of targetp. Their website only provides v2.0c as far as I can see.
Error in checkForRemoteErrors(val) :
2 nodes produced errors; first error: subscript contains invalid names
Run_mode - not very intuitive argument, make boolean and piper by default (?)
convention for status messages:
convention for error messages:
not safe currently:
currently parallel version of tmhmm is slower that the native tmhmm -> profile this
Error in names(sp) <- c("gene_id", "Cmax", "Cpos", "Ymax", "Ypos", "Smax", :
'names' attribute [12] must be the same length as the vector [5]
Higher level of abstraction for individual functions -> virtual wrapper/closure -> framework for integration of new tools? Would it make documentation more complex?
Alternative method for TM-prediction.
Stand-alone version lives here:
https://github.com/ElofssonLab/TOPCONS2
include more default arguments
Error:
Error in S4Vectors:::normalize_names_replacement_value(value, x) :
attempt to set too many names (1) on GroupedIRanges object of length 0
The same error persists even in the fasta extrcated with getOutfasta method
on top of default options for possible reverse functionality
revise examples, current example does not contain 'Signal peptide field'
upd examples, take into account all the new parameters and added functionality
isolate helper functions and source all of them (e.g crop_names)
Alternative method for TM-prediction.
Stand-alone version lives here:
https://github.com/ElofssonLab/TOPCONS2
Have been trying to run the example for signalp4 and it seems to run well, except the result is not returned, gor the same error with targetp.
step1_sp4 <- signalp(inp, version = 4,
organism = 'euk',
run_mode = "starter")
Output=
"Version used ... signalp4
Running signalp locally ...
2 sequences need to be truncated ...
Ok for single processing.
Submitted sequences... 100
Candidate sequences with signal peptides ... 3
Error in .wrap_in_length_one_list_like_object(value, names(x)[[i]], x) :
failed to coerce 'list(value)' to a AAStringSetList object of length 1"
Very nice package. Much appreciated.
There are third-party tools dependencies.
Do you plan to deliver a docker? Containers look like the natural solution for these package architectures.
Bests,
-A
Initialising site -----------------------------------------------------------------------------------
Copying '/home/anna/R/x86_64-pc-linux-gnu-library/3.4/pkgdown/assets/jquery.sticky-kit.min.js'
Copying '/home/anna/R/x86_64-pc-linux-gnu-library/3.4/pkgdown/assets/link.svg'
Copying '/home/anna/R/x86_64-pc-linux-gnu-library/3.4/pkgdown/assets/pkgdown.css'
Copying '/home/anna/R/x86_64-pc-linux-gnu-library/3.4/pkgdown/assets/pkgdown.js'
Building home ---------------------------------------------------------------------------------------
Error in xml2::xml_contents(heading)[[1]] : subscript out of bounds
vignettes: check that citations are correct and adequately formatted
missing entries?
sp2 outputs something weird as Cpos in the NN results: values > 100
so we will use a different line to extract cleavage position:
'Max cleavage site probability:' - should work for both signalp2 and signalp3 outputs
minimal documentation
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