BLASTDB v5 arch-dependency (was Re: [Help] metastudent keeps on failing on certain architectures)
Andreas Tille <andreas@an3as.eu> writes:
> I think it was some enhancement to follow Aarons hint to use blastdb
> format 5. However, the test keeps in failing for i386 and armhf
> architecture. For armhf the log[1] says:
Ugh, it looks like format 5 is architecture-dependent -- attempting to
point a 32-bit binary at a V5 database from a 64-bit binary fails with
Error: mdb_env_open: MDB_INVALID: File is not an LMDB file
even if I regenerate the database with BLASTDB_LMDB_MAP_SIZE set to a
32-bit-friendly value, as does attempting to point a 64-bit binary at a
V5 database from a 32-bit binary.
metastudent-data is far too large to make architecture-dependent if we
have any other recourse, so it looks like we should explicitly use V4
here after all; as previously noted, this would entail replacing the
formatdb command with
makeblastdb -dbtype prot -in "$<" -out "$(@:.psq=)"
I see a few other binary packages that contain BLAST databases and may
need similar treatment:
emboss-test (needs checking)
hhsuite (architecture-dependent, so presumably OK)
hmmer-examples (needs checking)
kleborate (architecture-dependent, so presumably OK)
ncbi-data (known safe, shipping pregenerated V4 databases)
ncbi-rrna-data (ditto)
openms-doc (needs checking)
staden-common (needs checking)
I'll take a closer look when I get a chance.
--
Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org)
http://www.mit.edu/~amu/ | http://stuff.mit.edu/cgi/finger/?amu@monk.mit.edu
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