The magicblast path is fixed and not portable

[hsiaoyi0504]

STREAMclean/mapper_wrapper.sh

Line 3 in 3d2347d

MAGIC_BLAST_DIR=/home/ubuntu/bastian/ncbi-magicblast-1.3.0

[hsiaoyi0504]

I think it will be good to use $PATH.

[gedankenstuecke]

This is just the default path, you can set your own by using the -m flag:

STREAMclean/mapper_wrapper.sh

Line 17 in 3d2347d

echo " -m magicBlastDir Specify the (existing) directory that contains the bin/magicblast - default is "$MAGIC_BLAST_DIR

[gedankenstuecke]

But I agree, it would be good to try and read from $PATH if it's there. Could run a which magicblast to find out whether it's there?

[hsiaoyi0504]

Or just write a setup.py and install a copy of that?