default /etc/ncbi/.ncbirc not read

[Tony Travis]

While attempting to use NCBI "blastn" from behind a proxy, I traced the execution of "blastn" to check if it was reading the default "/etc/ncbi/.ncbirc" config file where I put my proxy config because it wasn't working.

In fact, the default config file is never stat'ed or read:

> ajt@beluga:~$ strace blastn |& fgrep .ncbirc
> stat("./.ncbirc", 0x7fff8bbc0200) = -1 ENOENT (No such file or directory)
> stat("/home/ajt/.ncbirc", 0x7fff8bbc0200) = -1 ENOENT (No such file or directory)
> stat("/etc/.ncbirc", 0x7fff8bbc0200) = -1 ENOENT (No such file or directory)
> stat("/usr/bin/.ncbirc", 0x7fff8bbc0200) = -1 ENOENT (No such file or directory)

I created a "~/.ncbirc" file, which is read correctly, so I'm using that instead.

ProblemType: Bug
DistroRelease: Ubuntu 18.04
Package: ncbi-blast+ 2.6.0-1
ProcVersionSignature: Ubuntu 5.0.0-37.40~18.04.1-generic 5.0.21
Uname: Linux 5.0.0-37-generic x86_64
NonfreeKernelModules: zfs zunicode zavl icp zcommon znvpair wl
ApportVersion: 2.20.9-0ubuntu7.9
Architecture: amd64
CurrentDesktop: MATE
Date: Fri Jan 17 10:52:18 2020
InstallationDate: Installed on 2019-03-28 (295 days ago)
InstallationMedia: Ubuntu-MATE 18.04.2 LTS "Bionic Beaver" - Release amd64 (20190210)
SourcePackage: ncbi-blast+
UpgradeStatus: No upgrade log present (probably fresh install)

[Tony Travis (ajtravis)]

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".