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ropensci / phylotaR

An automated pipeline for retrieving orthologous DNA sequences from GenBank in R
https://docs.ropensci.org/phylotaR
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Unable to find correct versions of NCBI BLAST+ tools #40

Closed EricaBarroso closed 2 years ago

EricaBarroso commented 5 years ago

I am getting this error (last line):

library(phylotaR) wd <- /apps/Acanthaceae Error: unexpected '/' in "wd <- /" wd <- "/apps/Acanthaceae" ncbi_dr <- "/usr/lib/ncbi-blast+" txid <- 4185 setup(wd = wd, txid = txid, ncbi_dr = ncbi_dr, v = TRUE)

phylotaR: Implementation of PhyLoTa in R [v1.0.0]

Checking for valid NCBI BLAST+ Tools ... Failed to run: [/usr/lib/ncbi-blast+/makeblastdb]. Reason: [Error : Failed to execute '/usr/lib/ncbi-blast+/makeblastdb' (No such file or directory) ]Failed to run: [/usr/lib/ncbi-blast+/blastn]. Reason: [Error : Failed to execute '/usr/lib/ncbi-blast+/blastn' (No such file or directory) ]Error:Unable to find correct versions of NCBI BLAST+ tools Error in blast_setup(d = ncbi_dr, v = v, wd = wd) : Unable to find correct versions of NCBI BLAST+ tools

I think BLAST+ is ok in my computer. Perhaps I have to install some specific database? If I type: sudo apt install ncbi-blast+ I get: Reading package lists... Done Building dependency tree
Reading state information... Done ncbi-blast+ is already the newest version (2.6.0-1). 0 upgraded, 0 newly installed, 0 to remove and 83 not upgraded.

EricaBarroso commented 5 years ago

I made those directories (makeblastdb and blastn) and the error changed:

setup(wd = wd, txid = txid, ncbi_dr = ncbi_dr, v = TRUE)

phylotaR: Implementation of PhyLoTa in R [v1.0.0]

Checking for valid NCBI BLAST+ Tools ... Failed to run: [/usr/share/ncbi/data/makeblastdb]. Reason: [Error : Failed to execute '/usr/share/ncbi/data/makeblastdb' (Permission denied) ]Failed to run: [/usr/share/ncbi/data/blastn]. Reason: [Error : Failed to execute '/usr/share/ncbi/data/blastn' (Permission denied) ]Error:Unable to find correct versions of NCBI BLAST+ tools Error in blast_setup(d = ncbi_dr, v = v, wd = wd) : Unable to find correct versions of NCBI BLAST+ tools

I changed the permissions on the folder with the command: sudo chmod 777 ./ Still get the same error.

EricaBarroso commented 5 years ago

this was solved by placing R and wd folder in the same folder as blast

maelle commented 2 years ago

For info, we're looking for a new maintainer / a new maintainer team for this package, see #57 and feel free to volunteer, we'd be happy to help.