Installing problem with samtool headers

[mezi...@gmail.com]

Hello, I am trying to install Corset but it keeps not find finding the header files. I am using a new conda environment. I don't understand what is the problem. Thank you.

./configure --with-bam_inc=/media/sf_scratch/softwares/samtools

checking for g++... g++

checking whether the C++ compiler works... yes

checking for C++ compiler default output file name... a.out

checking for suffix of executables... 

checking whether we are cross compiling... no

checking for suffix of object files... o

checking whether we are using the GNU C++ compiler... yes

checking whether g++ accepts -g... yes

checking whether make sets $(MAKE)... yes

checking for /media/sf_scratch/scratch_Mert/Data_Mert/softwares/samtools/htslib-*.*/libhts.a... no

checking how to run the C++ preprocessor... g++ -E

checking for grep that handles long lines and -e... /bin/grep

checking for egrep... /bin/grep -E

checking for ANSI C header files... yes

checking for sys/types.h... yes

checking for sys/stat.h... yes

checking for stdlib.h... yes

checking for string.h... yes

checking for memory.h... yes

checking for strings.h... yes

checking for inttypes.h... yes

checking for stdint.h... yes

checking for unistd.h... yes

checking bam.h usability... no

checking bam.h presence... no

checking for bam.h... no

ERROR: Could not find the samtools headers.

       Please specify the location with: 

       './configure --with-bam_inc=<directory containing sam.h, bam.h etc.>

[Nadia Davidson]

Hi,

It maybe that conda doesn't install the headers and libraries when it installs samtools. You could try installing samtools manually from http://www.htslib.org/download/ and then pass the path to corset's config. Alternatively you can use the pre-compiled corset binaries if you are using linux.

Cheers,

Nadia.

[mezi...@gmail.com]

Thank you for your answer. Now I am relatively new to bioinformatics, so can I ask how can I use pre-compiled binaries? I am using linux but didn't see a 'corset' file in the cloned repository. If it will help me skip this problem, I would like to try this.

Cheers,

Mert Dogan

6 Eylül 2019 Cuma 01:08:33 UTC+2 tarihinde Nadia Davidson yazdı:

[Nadia Davidson]

Hi Mert,

You can download them from here, https://github.com/Oshlack/Corset/releases. Let us know if you run into any trouble.

Cheers,

Nadia.

[mezi...@gmail.com]

Hi Nadia,

Thank you for the link it worked fine. 

Cheers,

Mert

6 Eylül 2019 Cuma 23:09:28 UTC+2 tarihinde Nadia Davidson yazdı: