#20 minimus2-blat with hardcoded path to blat

[Thomas Sandmann]

When I tried to install amos in a non-standard location, minimus2-blat was looking for the blat executable in /usr/bin/blat despite my setting the BLAT environmental variable. It appears as if this behavior was hardcoded in the file src/Pipeline/minimus2-blat.acf.
Perhaps this could be changed ?

[smoretti]

I noticed the same thing for other variables, set at the configure step, not passed through all programs.
It happens for some $BASEDIR, BINDIR, NUCMER, BLAT, DELTAFILTER, SHOWCOORDS, show-tiling variables.

Also some programs have typos, or no more extension, when called from another program of the package. E.g. preTA.pl instead of preTA, ca2ta, ...

Some other calls are to package not mentioned at all in the documentation like Tigr Assembler, ...

Is there a new amos release planned soon?

[jw bargsten]

here is a patch for the DELTAFILTER and SHOWCOORDS variables. It seems that the variables are (1) either not substituted or (2) a required TAB character was replaced by a space in the configuration

[Jeff]

Thanks for the patch, it updated the path vars in minimus2!

If anyone could benefit from the steps so far:
first installed all dependencies, as needed

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd ~/git
git clone https://github.com/nathanhaigh/amos.git
cd amos

PATCH is needed (minimus2 will fail downstream, because of hardcoded paths)

from thread https://sourceforge.net/p/amos/bugs/20/

cd ~/git/amos
wget https://sourceforge.net/p/amos/bugs/_discuss/thread/a6a7b6be/9445/attachment/0001-bugfix-MUMmer-integration.patch
git apply 0001-bugfix-MUMmer-integration.patch

./bootstrap #creates a configure file
./configure --with-Boost-dir=/home/jcx9dy/bin/boost_1_58_0
make
make install
add ~/git/amos/bin to path in .bashrc

afterwards, check these files to make sure paths are proper:

patch succesfully fixed

/home/jcx9dy/git/amos/bin/minimus
/home/jcx9dy/git/amos/bin/minimus2
/home/jcx9dy/git/amos/bin/minimus2-blat

patch did not correct (not needed?)

/home/jcx9dy/git/amos/src/Pipeline/minimus.acf
/home/jcx9dy/git/amos/src/Pipeline/minimus2.acf
/home/jcx9dy/git/amos/src/Pipeline/minimus2-blat.acf

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

edit: minimus2 can detect paths correctly now; make sure to check bottom of run logs (where new log info is appended) if rerunning on same fasta file!