compilation error

[Maulik23]

I am trying to compile TMAP on ubuntu but getting following error:

src/util/../seq/../io/tmap_sam_io.h:79:1: error: unknown type name ‘sam_header_t’ In file included from src/util/tmap_definitions.c:14:0: src/util/../seq/tmap_seq.h:39:5: error: unknown type name ‘sam_header_record_t’ src/util/../seq/tmap_seq.h:40:5: error: unknown type name ‘sam_header_record_t’ src/util/../seq/tmap_seq.h:155:47: error: unknown type name ‘sam_header_t’ make[2]: * [src/util/tmap_definitions.o] Error 1 make[2]: Leaving directory `/home/ubuntu/Maulik/TMAP-master' make[1]: * [all-recursive] Error 1

please guide me for installtion

[iontorrent-dev]

You may have forgotten to follow the instructions in the README by not performing the git submodule init command. Please confirm you read the install instructions.

On Feb 22, 2013, at 1:31 AM, "Maulik23" notifications@github.com<mailto:notifications@github.com> wrote:

I am trying to compile TMAP on ubuntu but getting following error:

src/util/../seq/../io/tmap_sam_io.h:79:1: error: unknown type name ‘sam_header_t’ In file included from src/util/tmap_definitions.c:14:0: src/util/../seq/tmap_seq.h:39:5: error: unknown type name ‘sam_header_record_t’ src/util/../seq/tmap_seq.h:40:5: error: unknown type name ‘sam_header_record_t’ src/util/../seq/tmap_seq.h:155:47: error: unknown type name ‘sam_header_t’ make[2]: * [src/util/tmap_definitions.o] Error 1 make[2]: Leaving directory `/home/ubuntu/Maulik/TMAP-master' make[1]: * [all-recursive] Error 1

please guide me for installtion

— Reply to this email directly or view it on GitHubhttps://github.com/iontorrent/TMAP/issues/6.

[msturge]

I have encountered the same issue as above when compiling TMAP. I followed the steps listed on the site as:

git clone git://github.com/iontorrent/TMAP.git
cd TMAP
git checkout -b 3.0.1 tmap.3.0.1
git submodule init
git submodule update

At this point it hangs with the following.

$ git submodule update
Initialized empty Git repository in /path/to/my/TMAP/src/samtools/.git/

The above command does not complete.

I have also tried copying the samtools files into the src/ directory manually with the same results. And I have tried compiling samtools and htslib to another directory and specifying them in the ./configure script as CFlags='-I/path/to/samtools -I/path/to/htslib/include'.

All of these methods have resulted in the error mentioned above. What am I missing here?

Thank you.

[samfux84]

Hi,

same problem over here. When trying to run the "git submodule update", it hangs forever and does not complete. Have tried the same workaround as msturge by copying the samtools, bcftools and htslib sources to the "src" directory but then I get the same error messages as already documented by Maulik23.

Best regards

Sam

[plaw013]

Hi,

I too had the same issue with the git submodule update command hanging at the Initialization stage without any real helpful information. For me the fix was to edit the .git/config file in the TMAP directory and update the url of the [submodule "src/samtools"] section. In my case

[submodule "src/samtools"] url = http://github.com/nh13/samtools.git to [submodule "src/samtools"] url = https://github.com/nh13/samtools.git

Notice the https instead of http. Once this file was saved and the git submodule update command was executed again, the repository was successfully cloned and the compile, make, etc worked fine.

I also made the same adjustment to the .gitmodules file too...

Credit to rolf for his post here - https://ioncommunity.thermofisher.com/thread/4618 that led me on the right path...

Good luck.