[Nix-dev] Help packaging BLAST?
Jeffrey David Johnson
jefdaj at gmail.com
Wed Feb 25 06:30:13 CET 2015
Hi! The existing BLAST package (https://github.com/NixOS/nixpkgs/blob/master/pkgs/applications/science/biology/ncbi-tools/default.nix) isn't working for me. Probably because it's broken on x64. So I'm trying to package the standalone executables from http://www.ncbi.nlm.nih.gov/books/NBK52640/ instead. I've created a package (https://github.com/jefdaj/nixpkgs/blob/master/pkgs/applications/science/biology/ncbi-blast/default.nix) but can't run the resulting programs. They all say something like:
$ blastn
bash: /run/current-system/sw/bin/blastn: No such file or directory
Based on https://www.biostars.org/p/12298/ I think I have the right architecture:
$ uname -a
Linux acro 3.14.29 #1-NixOS SMP Thu Jan 1 00:00:01 UTC 1970 x86_64 GNU/Linux
$ file blastn
blastn: ELF 64-bit LSB executable, x86-64, version 1 (SYSV), dynamically linked (uses shared libs), for GNU/Linux 2.6.9, stripped
The "dynamically linked" part worries me though. Do I need to add build inputs referencing a specific gcc or something? Also including the suggested readelf command for completeness:
$ readelf -a blastn | head -n20
ELF Header:
Magic: 7f 45 4c 46 02 01 01 00 00 00 00 00 00 00 00 00
Class: ELF64
Data: 2's complement, little endian
Ident Version: 1 (current)
OS/ABI: UNIX - System V
ABI Version: 0
Type: EXEC (Executable file)
Machine: AMD x86-64
Version: 1 (current)
Entry point address: 0xc95f20
Start of program headers: 64 (bytes into file)
Start of section headers: 32499288 (bytes into file)
Flags:
Size of this header: 64 (bytes)
Size of program header entries: 56 (bytes)
Number of program headers entries: 9
Size of section header entries: 64 (bytes)
Number of section headers entries: 32
Section header string table index: 31
If this is a dead end, I could also try porting the Debian package right? How hard is that?
Thanks
Jeff
More information about the nix-dev
mailing list