A big use of space in 4273pi is the entire publicly available protein sequence database ('nr' from the NCBI, in BLAST format).
Does anyone actually want the entire protein sequence database in 4273pi?
It's fun, and mildly amazing, that it fits on an SD card at all. In practice, due to its size, it really takes too long to search on the Pi. The download also gets larger as more sequencing gets done. (SwissProt - a high-quality subset of the protein sequence database - will remain in 4273pi and is no problem.)
I've ordered the 'problematic' Sony SD card inder mentioned. I will test the next release of 4273pi on that; on the SanDisk card which we use extensively and is known to work (
http://eggg.st-andrews.ac.uk/files/2013 ... 4273pi.pdf); and the 'problematic' Intenso SD card. I put 'problematic' in quotes because I'm sure these are fine SD cards in general.
Finally, the work instruction ... I'm glad this is proving some use.
- As Alan said, it includes some hoops so I can use a static IP suited to my part of the University of St Andrews, yet set the card up to also work with DHCP. If you only want DHCP, the static IP stuff is not useful or important.
- I would suggest to use a large swapfile (script_3.sh). Some sources suggest this can eventually damage the SD card, but I'm not sure this is likely. More important, it's not nice to run out of address space.
- The entire protein sequence database gets uncompressed by script_6.sh. If it's now too big, try commenting-out ir deleting this part:
Code: Select all
echo Verifying and untarring nr BLAST database ...
echo
cd /home/pi/4273pi/blastdb || exit 1
for i in nr.*.gz
do
md5sum $i > $tmp || exit 1
cmp ${i}.md5 $tmp || exit 1
rm ${i}.md5 || exit 1
tar xzf $i || exit 1
rm $i || exit 1
echo $i - OK
done
echo ... OK
Thank you,
Daniel Barker
http://biology.st-andrews.ac.uk/staff/db60