Trouble compiling ABySS from source

Question

[jordanashworth492]

Hi,

I'm trying to run abyss-sealer but with the normal installation (sudo apt-get install abyss), I can't get it to work. It doesn't recognize the command. So I'm trying to compile from source instead but I can't get pass the make step. It's throwing me errors stating it can't find -lsqlite3. So I reran ./configure pointing to the location of sqlite but I keep getting the same errors. Does anyone know where I'm going wrong?

./configure --with-sqlite=/usr/bin/sqlite

checking sqlite3.h usability... no

checking sqlite3.h presence... no

checking for sqlite3.h... no

checking for main in -lsqlite3... no

make

/usr/bin/ld: cannot find -lsqlite3

Also if anyone has any idea as to why I cant' get abyss-sealer to work on the normal installation, your input would be much appreciated. The test case worked fine with the regular abyss command.

Thanks,

Jordan

[Jean-Karim Heriche]

There could be several reasons why it couldn't find sqlite3. Your configure option is pointing to sqlite not sqlite3 so make sure you have installed sqlite3 first.

[StarCute]

Install the required dependencies mentioned in the documentation.

Answer 1

[benv]

Hi Jordan,

Sorry for the trouble. Please see https://github.com/bcgsc/abyss/issues/86 for some tips on getting it to compile.

Answer 2

[kloetzl]

/usr/bin/sqlite is the sqlite executable i.e. program. However, that configure script is looking for the sqlite library. Specifically needs a header sqlite.h and something to link against -lsqlite3. Try installing the library version of sqlite!

[Jean-Karim Heriche]

sqlite and sqlite3 are not the same thing. On Ubuntu at least, sqlite means sqlite version 2.

Answer 3

[SES]

The --with-sqlite option should point to the sqlite directory, not the executable. The configure script is looking for the lib directory and headers in that location and not finding them (as shown in your error message). If you installed the sqlite-dev (or whatever it's called) package, then you don't need to give this option. If you want to compile it locally without installing sqlite in a system path then this is probably necessary. Though, I'm not sure you can configure this locally from source because of boost but it may be possible. This is not a direct answer, but you may want to see if there are binaries available for your system.