The BUG appears to be caused when the NCBI environment variable is
undefined. Setting NCBI to the installed location of the default config
file under Ubuntu fixes the problem:
> ajt@beluga:~$ export NCBI=/etc/ncbi
> ajt@beluga:~$ strace blastn |& fgrep .ncbirc
> stat("./.ncbirc", 0x7ffc01d0e2c0) = -1 ENOENT (No such file or
> directory)
> stat("/home/ajt/.ncbirc", 0x7ffc01d0e2c0) = -1 ENOENT (No such file or
> directory)
> stat("/etc/ncbi/.ncbirc", {st_mode=S_IFREG|0644, st_size=1229, ...}) = 0
> stat("/etc/ncbi/.ncbirc", {st_mode=S_IFREG|0644, st_size=1229, ...}) = 0
> stat("/etc/ncbi/.ncbirc", {st_mode=S_IFREG|0644, st_size=1229, ...}) = 0
> lstat("/etc/ncbi/.ncbirc", {st_mode=S_IFREG|0644, st_size=1229, ...}) = 0
> openat(AT_FDCWD, "/etc/ncbi/.ncbirc", O_RDONLY) = 3
> stat("./.ncbirc", 0x7ffc01d0eae0) = -1 ENOENT (No such file or
> directory)
> stat("/home/ajt/.ncbirc", 0x7ffc01d0eae0) = -1 ENOENT (No such file or
> directory)
> stat("/etc/ncbi/.ncbirc", {st_mode=S_IFREG|0644, st_size=1229, ...}) = 0
This behaviour is consistent to what NCBI describe:
> https://www.ncbi.nlm.nih.gov/books/NBK279695/
If the NCBI variable is unset, "blastn" looks for "/etc/.ncbirc".
However, the default location the config file is installed to under
Ubuntu is "/etc/ncbi/.ncbirc".
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https://bugs.launchpad.net/bugs/1860109
Title:
default /etc/ncbi/.ncbirc not read
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