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I am trying to analyze some Primers with R but it seems openPrimeR can't find MELTING even though it is installed. Am I missing something obvious?
library(openPrimeR)
There are missing/non-functioning external tools.
To use the full potential of openPrimeR, please make sure
that the required versions of the speciied tools are
installed and that they are functional:
o MELTING (http://www.ebi.ac.uk/biomodels/tools/melting/)
The number of cores for was set to '2' by 'parallel_setup()'.
sessionInfo( )
R version 4.1.0 (2021-05-18)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.2 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
locale:
[1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C
[3] LC_TIME=de_DE.UTF-8 LC_COLLATE=de_DE.UTF-8
[5] LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=de_DE.UTF-8
[7] LC_PAPER=de_DE.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] openPrimeR_1.14.0
loaded via a namespace (and not attached):
[1] Rcpp_1.0.7 plyr_1.8.6 RColorBrewer_1.1-2
[4] pillar_1.6.1 compiler_4.1.0 GenomeInfoDb_1.28.1
[7] XVector_0.32.0 iterators_1.0.13 zlibbioc_1.38.0
[10] tools_4.1.0 bitops_1.0-7 lifecycle_1.0.0
[13] tibble_3.1.2 gtable_0.3.0 pkgconfig_2.0.3
[16] rlang_0.4.11 foreach_1.5.1 rstudioapi_0.13
[19] DBI_1.1.1 parallel_4.1.0 GenomeInfoDbData_1.2.6
[22] stringr_1.4.0 dplyr_1.0.7 generics_0.1.0
[25] Biostrings_2.60.1 vctrs_0.3.8 S4Vectors_0.30.0
[28] IRanges_2.26.0 stats4_4.1.0 grid_4.1.0
[31] tidyselect_1.1.1 glue_1.4.2 R6_2.5.0
[34] fansi_0.5.0 reshape2_1.4.4 ggplot2_3.3.5
[37] purrr_0.3.4 magrittr_2.0.1 codetools_0.2-18
[40] GenomicRanges_1.44.0 scales_1.1.1 ellipsis_0.3.2
[43] BiocGenerics_0.38.0 assertthat_0.2.1 colorspace_2.0-2
[46] utf8_1.2.1 stringi_1.7.3 lpSolveAPI_5.5.2.0-17.7
[49] doParallel_1.0.16 RCurl_1.98-1.3 munsell_0.5.0
[52] crayon_1.4.1
Newest version of MELTING is installed and executables are in PATH
(base) ngs-benedikt@ngsbenedikt-desktop:~$ melting -V
This MELTING program is the version 5.2.0.
Thanks!
openPrimeR requires and checks for
melting-batch
rather thanmelting
. Could you verify whether that's in your PATH as well?