On 24 February 2015 at 21:30, Jeffrey David Johnson <[email protected]> wrote: > 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
You probably have to run some patchelf command. Take a look at networking/browsers/firefox-bin maybe (the firefox expression that just downloads the official binary). James _______________________________________________ nix-dev mailing list [email protected] http://lists.science.uu.nl/mailman/listinfo/nix-dev
