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smarco / gem3-mapper

GEM-Mapper v3
GNU General Public License v3.0
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compilation failed #4

Closed lmanchon closed 6 years ago

lmanchon commented 6 years ago

--Hi,

some problem at compilation step in source file:

gcc -O2 -DNDEBUG -I../../../include -c match_align_normalize.c -o ../../../build/match_align_normalize.o match_align_normalize.c: In function ‘match_align_normalize_cigar’: match_align_normalize.c:108: error: unknown field ‘length’ specified in initializer match_align_normalize.c:109: error: unknown field ‘length’ specified in initializer

thank you --

smarco commented 6 years ago

Hi,

It's weird because as far as I can tell we never compile using -O2 option. Can you please try again to clone the repository and compile from scratch? If you still get this error, please send me the command line used and your system specs so we can solve your problem.

Thanks for the report. Cheers,

El 19 ene. 2018 12:07 p. m., "lmanchon" notifications@github.com escribió:

--Hi,

some problem at compilation step in source file:

gcc -O2 -DNDEBUG -I../../../include -c match_align_normalize.c -o ../../../build/match_align_normalize.o match_align_normalize.c: In function ‘match_align_normalize_cigar’: match_align_normalize.c:108: error: unknown field ‘length’ specified in initializer match_align_normalize.c:109: error: unknown field ‘length’ specified in initializer

thank you --

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lmanchon commented 6 years ago

ok, good i have loaded gcc-4.9.1 and now it compiled fine. The error was due to the fact that some old compilers version don't accept the -Ofast option. I have changed it to a more general -O2 option and then compile with gcc-4.6.2, some object files are compiled but others not. Laurent --

smarco commented 6 years ago

Ok, great. We will add a minimum requirements list.

Thanks,

El 19 ene. 2018 12:19 p. m., "lmanchon" notifications@github.com escribió:

ok, good i have loaded gcc-4.9.1 and now it compiled fine. The error was due to the fact that some old compilers version don't accept the -Ofast option. I have changed it to a more general -O2 option and then compile with gcc-4.6.2, some object files are compiled but others not. Laurent --

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lmanchon commented 6 years ago

Sorry i have a question about the .csv file i need to use, i have fastq.gz files and i don't understand what 'flowcell,lane,index' means, can you give me an explicit example please ? thank you --

smarco commented 6 years ago

In principle, there is no need to use any cvs file in order tu perform regular sequence mapping. Just provide the mapper with the fastq.gz file. README should give a brief example of this.

Let me know.

El 19 ene. 2018 12:30 p. m., "lmanchon" notifications@github.com escribió:

Sorry i have a question about the .csv file i need to use, i have fastq.gz files and i don't understand what 'flowcell,lane,index' means, can you give me an explicit example please ? thank you --

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lmanchon commented 6 years ago

i thought about gemBS: http://statgen.cnag.cat/GEMBS/UserGuide/_build/html/pipelineSteps.html

smarco commented 6 years ago

Ah, ok. Bear in mind that the framework GEMBS is another project, despite using GEM3 to perform the mapping.

The CVS file is used by GEMBS to include the proper metadata information into the SAM/BAM files generated (i.e. sample,library,flowcell,lane,index). The GEMBS documentation gives an example:

tissue_1,lib_1,flowcell_A,1,1tissue_1,lib_1,flowcell_A,2,1tissue_1,lib_1,flowcell_A,3,1tissue_2,lib_2,flowcell_A,4,1tissue_2,lib_2,flowcell_A,5,1tissue_3,lib_1,flowcell_B,1,1

Let me know if that helps. Cheers,

El 19 ene. 2018 12:38 p. m., "lmanchon" notifications@github.com escribió:

i thought about gemBS: http://statgen.cnag.cat/GEMBS/ UserGuide/_build/html/pipelineSteps.html

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lmanchon commented 6 years ago

ok, thank you so much.