rmap installation

[Tommaso Andreani]

Hello,

I have downloaded MethPipe (last vestion methpipe-3.4.3.tar.bz2 (release history)).

I have realized when I have tested the data that the mapper is not installed (rmap). So I have downloaded it from here:

https://github.com/smithlabcode/rmap

After unzipping and doing:

Make install

I have the following errors:

make[1]: Entering directory `/fsimb/imbc_home/tandrean/WGBS/rmap-master/src/mappers'

make[2]: Entering directory `/fsimb/imbc_home/tandrean/WGBS/rmap-master/src/mappers/rmap'

g++ -Wall -fPIC -fmessage-length=50 -O3 -c -o ../../common/SeedMaker.o ../../common/SeedMaker.cpp -I../../common -I/src/smithlab_cpp/

../../common/SeedMaker.cpp:26:30: fatal error: smithlab_utils.hpp

   : No such file or directory

compilation terminated.

make[2]: *** [../../common/SeedMaker.o] Error 1

make[2]: Leaving directory `/fsimb/imbc_home/tandrean/WGBS/rmap-master/src/mappers/rmap'

make[2]: Entering directory `/fsimb/imbc_home/tandrean/WGBS/rmap-master/src/mappers/rmapbs'

g++ -Wall -fPIC -fmessage-length=50 -O3 -c -o ../../common/SeedMaker.o ../../common/SeedMaker.cpp -I../../common -I/src/smithlab_cpp/

../../common/SeedMaker.cpp:26:30: fatal error: smithlab_utils.hpp

   : No such file or directory

compilation terminated.

make[2]: *** [../../common/SeedMaker.o] Error 1

make[2]: Leaving directory `/fsimb/imbc_home/tandrean/WGBS/rmap-master/src/mappers/rmapbs'

make[1]: *** [all] Error 2

make[1]: Leaving directory `/fsimb/imbc_home/tandrean/WGBS/rmap-master/src/mappers'

make[1]: Entering directory `/fsimb/imbc_home/tandrean/WGBS/rmap-master/src/simulation'

make[2]: Entering directory `/fsimb/imbc_home/tandrean/WGBS/rmap-master/src/simulation/simreads'

make[2]: *** No rule to make target `/src/smithlab_cpp//sim_utils.o', needed by `simreads'.  Stop.

make[2]: Leaving directory `/fsimb/imbc_home/tandrean/WGBS/rmap-master/src/simulation/simreads'

make[2]: Entering directory `/fsimb/imbc_home/tandrean/WGBS/rmap-master/src/simulation/simreadsbs'

make[2]: *** No rule to make target `/src/smithlab_cpp//sim_utils.o', needed by `simreadsbs'.  Stop.

make[2]: Leaving directory `/fsimb/imbc_home/tandrean/WGBS/rmap-master/src/simulation/simreadsbs'

make[2]: Entering directory `/fsimb/imbc_home/tandrean/WGBS/rmap-master/src/simulation/simreadspe'

make[2]: *** No rule to make target `/src/smithlab_cpp//sim_utils.o', needed by `simreadspe'.  Stop.

make[2]: Leaving directory `/fsimb/imbc_home/tandrean/WGBS/rmap-master/src/simulation/simreadspe'

make[1]: *** [all] Error 2

make[1]: Leaving directory `/fsimb/imbc_home/tandrean/WGBS/rmap-master/src/simulation'

make[1]: Entering directory `/fsimb/imbc_home/tandrean/WGBS/rmap-master/src/utils'

make[1]: *** No targets specified and no makefile found.  Stop.

make[1]: Leaving directory `/fsimb/imbc_home/tandrean/WGBS/rmap-master/src/utils'

make: *** [all] Error 2

Does anyone have faced a similar problem during the installation of this tool?

Thanks in advance.

Tommaso

[Jianghan Qu]

Hi Tommaso, 

It seems that the zipped version doesn't contain smithlab_cpp. 

You can clone the directory with the following command 

git clone --recursive https://github.com/smithlabcode/rmap.git

so that the smithlab_cpp module is downloaded together with rmap. 

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Jenny

[Tommaso Andreani]

oh thanks. another question but is it possible that the command "walt" does the same thing of rmap? 

thanks again. Tomorrow I will try to install with git the aligner. 

Cheers

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[Jianghan Qu]

Yes, both rmap and walt are mappers for BS-seq reads.  In my experience, walt is faster.