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smehringer / SViper

Swipe your Structural Variants called on long (ONT/PacBio) reads with short exact (Illumina) reads.
BSD 3-Clause "New" or "Revised" License
32 stars 8 forks source link

Installation error #20

Open aserres opened 3 years ago

aserres commented 3 years ago

Hi,

Thank you for your contribution with SViper, we are trying to apply it to polish structural variants called using ONT in humans.

I'm encountering an error trying to install SViper in a slurm/lustre cluster system. Note that my GCC version (6.3.0) is not the recommended, but I do not have access to another. Could that be the cause of the problem? I'd welcome any input to try to fix the issue.

Attached is the full error report:

[aserres@login1 build]$ cmake ../ -- The CXX compiler identification is GNU 6.3.0 -- Check for working CXX compiler: /apps/GCC/6.3.0/bin/c++ -- Check for working CXX compiler: /apps/GCC/6.3.0/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done source dir: /scratch/devel/aserres/bin/SViper -- These dependencies were found: OPENMP TRUE -fopenmp ZLIB TRUE 1.2.3 SEQAN TRUE 2.4.0 -- The requirements were met. -- Configuring done -- Generating done -- Build files have been written to: /scratch/devel/aserres/bin/SViper/build [aserres@login1 build]$ make sviper Scanning dependencies of target sviper [ 50%] Building CXX object CMakeFiles/sviper.dir/src/sviper.cpp.o In file included from /scratch/devel/aserres/bin/SViper/extern/seqan/include/seqan/basic.h:101:0, from /scratch/devel/aserres/bin/SViper/extern/seqan/include/seqan/bam_io.h:46, from /scratch/devel/aserres/bin/SViper/include/sviper/basics.h:9, from /scratch/devel/aserres/bin/SViper/include/sviper/auxiliary.h:2, from /scratch/devel/aserres/bin/SViper/include/sviper/io.h:7, from /scratch/devel/aserres/bin/SViper/src/sviper.cpp:1: /scratch/devel/aserres/bin/SViper/include/sviper/sviper.h: In function ‘bool sviper::polish_variant(sviper::Variant&, sviper::input_output_information&)’: /scratch/devel/aserres/bin/SViper/extern/seqan/include/seqan/basic/basic_tangle.h:43:15: error: ‘viewRecords’ is not a member of ‘seqan’

define seqan seqan

           ^

/scratch/devel/aserres/bin/SViper/include/sviper/sviper.h:221:9: note: in expansion of macro ‘seqan’ seqan::viewRecords(long_reads, long_read_bam, info.long_read_bai, rID_long, var_ref_pos_sub50, var_ref_pos_add50); ^ /scratch/devel/aserres/bin/SViper/extern/seqan/include/seqan/basic/basic_tangle.h:43:15: error: ‘viewRecords’ is not a member of ‘seqan’

define seqan seqan

           ^

/scratch/devel/aserres/bin/SViper/include/sviper/sviper.h:223:9: note: in expansion of macro ‘seqan’ seqan::viewRecords(long_reads, long_read_bam, info.long_read_bai, rID_long, var_ref_pos_end_sub50, var_ref_pos_end_add50); ^ /scratch/devel/aserres/bin/SViper/extern/seqan/include/seqan/basic/basic_tangle.h:43:15: error: ‘viewRecords’ is not a member of ‘seqan’

define seqan seqan

           ^

/scratch/devel/aserres/bin/SViper/include/sviper/sviper.h:379:17: note: in expansion of macro ‘seqan’ seqan::viewRecords(short_reads, short_read_bam, info.short_read_bai, rID_short, ref_region_start, e); ^ /scratch/devel/aserres/bin/SViper/extern/seqan/include/seqan/basic/basic_tangle.h:43:15: error: ‘viewRecords’ is not a member of ‘seqan’

define seqan seqan

           ^

/scratch/devel/aserres/bin/SViper/include/sviper/sviper.h:385:17: note: in expansion of macro ‘seqan’ seqan::viewRecords(tmp_short_reads, short_read_bam, info.short_read_bai, rID_short, s, ref_region_end); ^ /scratch/devel/aserres/bin/SViper/extern/seqan/include/seqan/basic/basic_tangle.h:43:15: error: ‘viewRecords’ is not a member of ‘seqan’

define seqan seqan

           ^

/scratch/devel/aserres/bin/SViper/include/sviper/sviper.h:392:17: note: in expansion of macro ‘seqan’ seqan::viewRecords(short_reads, short_read_bam, info.short_read_bai, rID_short, ref_region_start, ref_region_end); ^ /scratch/devel/aserres/bin/SViper/extern/seqan/include/seqan/basic/basic_tangle.h:43:15: error: ‘ConvexGaps’ is not a member of ‘seqan’

define seqan seqan

           ^

/scratch/devel/aserres/bin/SViper/include/sviper/sviper.h:460:28: note: in expansion of macro ‘seqan’ seqan::ConvexGaps()); ^ make[3]: [CMakeFiles/sviper.dir/src/sviper.cpp.o] Error 1 make[2]: [CMakeFiles/sviper.dir/all] Error 2 make[1]: [CMakeFiles/sviper.dir/rule] Error 2 make: [sviper] Error 2

Anzy-99 commented 2 years ago

Hi, I'm having the same installation problem as you. If you have solved the problem, can you tell me how to do it? Thanks!

smehringer commented 2 years ago

Hi @aserres and @Anzy-99,

I'm very sorry to get back to you so late but I was on maternity leave this year until a few weeks ago.

Let's trouble shoot.

First: When cloning SViper, did you use the git option --recurse-submodules? If not or if you are not sure. Go to the SViper directory and type

git submodule update --init

Remove everything in the build directory and try using cmake and make again.

shwetaramdas commented 2 years ago

I'm having the same problem on my system. I didn't use 'git clone' to get SViper on my machine, but downloaded the zip from Github, and unzipped, and then followed the instructions (mkdir build --> cmake ../ --> make sviper)

I added the include path from my seqan installation to CMAKE_PREFIX_PATH, but I get the same error as in the original post. Any leads on why this might be? Thank you!

joelfnogueira commented 8 months ago

For me works these way: git clone https://github.com/smehringer/SViper.git micromamba install -c bioconda seqan micromamba install -c conda-forge cxx-compiler micromamba install -c anaconda cmake cd SViper git submodule update --init mkdir build cd build cmake .. make sviper