I have struggled a long time to install Dindel on Mac and finally got it installed. I just write it down. Hope this is helpful to others. Many thanks to Kees Albers and csoong. The information they provide helps me a lot.
Please also read cscong's thread.
My Mac is version 10.6.5. To install Dindel on your Mac:
1) install samtools (the samtools need to be compiled)
2) install boost library
After untar the tarball, you need to go into the directory("boost_1_45_0" in my case) and run:
./bootstrap.sh -prefix=DIR_PATH
./bjam install
This will take a while and all boost binaries(library) and headers will installed
under DIR_PATH (subdirectory lib/ contains boost binaries and include/ contains boost headers).
3) install Dindel
Note: please download the src file ("dindel-1.01-src.tar.gz" in my case).
Untar the file and go into the directory ("dindel-1.01-src" in my case).
Open "MakeFile" in a text editor and change some places as what cscong said (cscong has pasted his/her MakeFile in that thread). Basically:
- add the path to the samtools you installed
- remove static flag
- add boost lib/ and include/ in "CXXFLAGS" and add boost lib/ in "LDFLAGS", These directories are "/opt/local/lib/" and "/opt/local/lib/" in cscong case. If you follow my way to install boost, the lib/ and include/ directory should under directory "DIR_PATH" you provided.
now you can type "make" in the Dindel directory and run. After this, you will see dindel executable file.
In general, this should be enough now. However, in my case, when I run dindel, I got error message "can not loading library ...", so I copy the following two files from boost lib/ to the Dindel directory:
libboost_program_options.dylib
libboost_thread.dylib
Then I can run dindel
Note:
1) By installation of dindel in this way, all python scripts (eg. makeWindows.py) are not included automatically. You need to get those by downloading linux or mac-version of installation files (for example: dindel-1.01-mac-os-x.tar.gz). (Many thanks to Ida to let me know this)
2) In my case, I can not call dindel from other directories in the system, since the system doesn't know where to find the "dylib" files. One way to get around this is to copy "libboost_program_options.dylib" and "libboost_thread.dylib" to where I want to call dindel. Otherwise, I will still get error message of "can not loading library".
Please also read cscong's thread.
My Mac is version 10.6.5. To install Dindel on your Mac:
1) install samtools (the samtools need to be compiled)
2) install boost library
After untar the tarball, you need to go into the directory("boost_1_45_0" in my case) and run:
./bootstrap.sh -prefix=DIR_PATH
./bjam install
This will take a while and all boost binaries(library) and headers will installed
under DIR_PATH (subdirectory lib/ contains boost binaries and include/ contains boost headers).
3) install Dindel
Note: please download the src file ("dindel-1.01-src.tar.gz" in my case).
Untar the file and go into the directory ("dindel-1.01-src" in my case).
Open "MakeFile" in a text editor and change some places as what cscong said (cscong has pasted his/her MakeFile in that thread). Basically:
- add the path to the samtools you installed
- remove static flag
- add boost lib/ and include/ in "CXXFLAGS" and add boost lib/ in "LDFLAGS", These directories are "/opt/local/lib/" and "/opt/local/lib/" in cscong case. If you follow my way to install boost, the lib/ and include/ directory should under directory "DIR_PATH" you provided.
now you can type "make" in the Dindel directory and run. After this, you will see dindel executable file.
In general, this should be enough now. However, in my case, when I run dindel, I got error message "can not loading library ...", so I copy the following two files from boost lib/ to the Dindel directory:
libboost_program_options.dylib
libboost_thread.dylib
Then I can run dindel
Note:
1) By installation of dindel in this way, all python scripts (eg. makeWindows.py) are not included automatically. You need to get those by downloading linux or mac-version of installation files (for example: dindel-1.01-mac-os-x.tar.gz). (Many thanks to Ida to let me know this)
2) In my case, I can not call dindel from other directories in the system, since the system doesn't know where to find the "dylib" files. One way to get around this is to copy "libboost_program_options.dylib" and "libboost_thread.dylib" to where I want to call dindel. Otherwise, I will still get error message of "can not loading library".
Comment