installation of abyss-1.9.0

[Yifang Tan]

Hello group:

I had problem with installation of abyss-1.9.0.

$ ./configure --prefix=/home/yifang/Downloads/abyss-1.9.0 --with-boost=/usr/include --with-mpi=/usr/lib/openmpi --enable-maxk=128

$ make -j12

rm -f libdb.a
ar cru libdb.a libdb_a-DB.o ../Common/libcommon.a
ar: `u' modifier ignored since `D' is the default (see `U')
/usr/bin/ld: cannot find -lsqlite3
ranlib libdb.a
collect2: error: ld returned 1 exit status
Makefile:389: recipe for target 'abyss-db-csv' failed
make[2]: *** [abyss-db-csv] Error 1
make[2]: *** Waiting for unfinished jobs....
make[2]: Leaving directory '/home/yifang/download-software/abyss-1.9.0/DataBase'
Makefile:445: recipe for target 'all-recursive' failed
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory '/home/yifang/download-software/abyss-1.9.0'
Makefile:364: recipe for target 'all' failed
make: *** [all] Error 2

I thought the problem is the sqlite3.

$locate sqlite3

/usr/lib/x86_64-linux-gnu/libsqlite3.so.0
/usr/lib/x86_64-linux-gnu/libsqlite3.so.0.8.6
/usr/lib/x86_64-linux-gnu/apr-util-1/apr_dbd_sqlite3-1.so
/usr/lib/x86_64-linux-gnu/apr-util-1/apr_dbd_sqlite3.so

so I designated the path and configure with:

$ ./configure --prefix=/home/yifang/Downloads/abyss-1.9.0 --with-boost=/usr/include --with-mpi=/usr/lib/openmpi --with-sqlite=/usr/lib/x86_64-linux-gnu --enable-maxk=128

$make -j12

Uncompress.cpp: In function ‘bool uncompress_init()’:
Uncompress.cpp:220:9: error: ‘HAVE_LIBDL’ was not declared in this scope
  return HAVE_LIBDL;
         ^
mv -f .deps/libcommon_a-Options.Tpo .deps/libcommon_a-Options.Po
Makefile:512: recipe for target 'libcommon_a-Uncompress.o' failed
make[2]: *** [libcommon_a-Uncompress.o] Error 1
make[2]: *** Waiting for unfinished jobs....
mv -f .deps/libcommon_a-Fcontrol.Tpo .deps/libcommon_a-Fcontrol.Po
......
make[2]: Leaving directory '/home/yifang/download-software/abyss-1.9.0/Common'
Makefile:445: recipe for target 'all-recursive' failed
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory '/home/yifang/download-software/abyss-1.9.0'
Makefile:364: recipe for target 'all' failed
make: *** [all] Error 2

Any clue on this error is appreciated!

yt

[Ben Vandervalk]

Hi Yifang,

Sorry about this.  To get rid of the annoying sqlite3 problems, I would recommend using the HEAD version of ABySS from github rather than ABySS 1.9.0. See here for further comments on this issue: https://github.com/bcgsc/abyss

- Ben

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[Ben Vandervalk]

Sorry, I pasted the wrong link.  Here is the correct one:

https://github.com/bcgsc/abyss/issues/86

- Ben

[Yifang Tan]

Thanks!

The problem has been resolved now following to the new link.

Best regards,

Yifang