Question: Augustus install mac
gravatar for Max Haase
4.8 years ago by
Max Haase40
UW Madison
Max Haase40 wrote:

I'm trying to compile AUGUSTUS on my mac (10.10.4) and I fail to compile bam2hints and filterBam executables. I get this error: g++ -Wall -O2 -c -o bam2hints.o -I/usr/include/bamtools fatal error: 'api/BamReader.h' file not found include <api bamreader.h="">

1 error generated. make[2]: * [bam2hints.o] Error 1 make[1]: [all] Error 2 make: ** [all] Error 2

I have installed bamtools and I know for a fact that api/BamReader.h is there despite it saying it isn't.


software error genome • 4.5k views
ADD COMMENTlink modified 4.7 years ago by Jon340 • written 4.8 years ago by Max Haase40
gravatar for Jon
4.7 years ago by
United States - US FS
Jon340 wrote:

You have to make changes to the Makefiles for both bam2hints and filterBam to explicitly state where your bamtools installation files are. The easier way to install is to use homebrew.

To manually edit the makefiles you will need to add the following to the auxprogs/filterBam/src/Makefile:

BAMTOOLS = /your/path/to/bamtools

And then also make sure that under the INCLUDE variable that it is pointing to the correct folder that houses the api/bamreader.h. For example, if you installed bamtools from home-brew, the includes are in a slightly different place.

You also need to edit the path to the BAMTOOLS variable in the auxprogs/bam2hints/Makefile.

Given all of this, I still have had problems getting Augustus to install correctly, lately I've had problems using the --proteinprofile functionality - and I think some of the issues are compilation specific, i.e. just seem to happen on Mac and not Linux.

ADD COMMENTlink written 4.7 years ago by Jon340

Thanks Jon for the advice! I was able to compile bam2hits and filterBam successfully and it appears that augustus is working properly.

ADD REPLYlink written 4.7 years ago by Max Haase40

Just thought it may be useful to others, I put my comment here. In my case, gcc version also matters. gcc4.8 works for bam2hints but not filterbam. I used gcc5.4 to compile filterbam successfully.

ADD REPLYlink written 4.2 years ago by shl198410

I had a similar error, and in the end, I found a detailed step-by-step manual to correct this error, which is based on this answer.

Edit: After following this manual, it gave me the same error, but at least it seems like I can run the program from the augustus/src/ directory.

ADD REPLYlink modified 3.6 years ago • written 3.6 years ago by Tye Kahn10

I've edited the makefile (filterbam/src)as you mentioned, but again it shows the same error.

make[3]: Entering directory `/home/dcb/Documents/EV/Maker/augustus-3.3.2/auxprogs/filterBam/src'
g++     -std=c++0x  -c -o filterBam.o -I/home/dcb/Documents/EV/Maker/bamtools/include/bamtools -Iheaders -I./bamtools fatal error: api/BamReader.h: No such file or directory
 #include <api/BamReader.h>    
compilation terminated.
make[3]: *** [filterBam.o] Error 1
ADD REPLYlink modified 18 months ago • written 18 months ago by ashaneev0720

I had the similar error, and I finally solved it by installing Augustus via conda.

ADD REPLYlink written 18 months ago by IrisChang10
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