SeqMule installation

[slma2021]

Hi,

I am new to SeqMule and Ubuntu. I tried to install SeqMule to my pc
I used the following to install
git clone https://github.com/WGLab/SeqMule.git
#if HTTPS is not supported, use git protocol instead
#git clone git://github.com/WGLab/SeqMule.git
cd SeqMule
./Build freshinstall

Also follow the instruction on installing prerequisities

I go to SeqMule folder and try to run the followings
seqmule download -down hg19all

it said
SeqMule: command not found

I tried the command with different version, like SeqMule, seqmule, ./SeqMule, ./seqmule

I am not sure which step run wrong

please kindly help!

in addition, if I only want to do Trio exome analysis, do I need to download database?

thanks a lot in advance

Best regards,
Suk Ling MA

[slma2021]

I now can install SeqMule but it said I missed some programs, such as vcftools
ry.cpp: In member function ‘void entry::make_typed_float_vector(std::vector&, const string&, int)’:
entry.cpp:594:43: error: narrowing conversion of ‘128’ from ‘int’ to ‘char’ [-Wnarrowing]
594 | char missing[4] = {0x01, 0x00, 0x80, 0x7F};
| ^
entry.cpp:595:39: error: narrowing conversion of ‘128’ from ‘int’ to ‘char’ [-Wnarrowing]
595 | char end[4] = {0x02, 0x00, 0x80, 0x7F};
| ^
entry.cpp: In member function ‘void entry::make_typed_float_vector(std::vector&, const std::vector<std::__cxx11::basic_string >&, int)’:
entry.cpp:657:43: error: narrowing conversion of ‘128’ from ‘int’ to ‘char’ [-Wnarrowing]
657 | char missing[4] = {0x01, 0x00, 0x80, 0x7F};
| ^
entry.cpp:658:39: error: narrowing conversion of ‘128’ from ‘int’ to ‘char’ [-Wnarrowing]
658 | char end[4] = {0x02, 0x00, 0x80, 0x7F};
| ^
entry.cpp: In member function ‘bool entry::check_missing(unsigned int, unsigned int, const std::vector&)’:
entry.cpp:872:56: error: narrowing conversion of ‘128’ from ‘int’ to ‘char’ [-Wnarrowing]
872 | static char missing_float[4] = {0x01, 0x00, 0x80, 0x7F};
| ^
entry.cpp:874:43: error: narrowing conversion of ‘128’ from ‘int’ to ‘char’ [-Wnarrowing]
874 | static char missing_int2[2] = {0x00, 0x80};
| ^
entry.cpp:875:55: error: narrowing conversion of ‘128’ from ‘int’ to ‘char’ [-Wnarrowing]
875 | static char missing_int3[4] = {0x00, 0x00, 0x00, 0x80};
| ^
entry.cpp: In member function ‘bool entry::check_end(unsigned int, unsigned int, const std::vector&)’:
entry.cpp:931:52: error: narrowing conversion of ‘128’ from ‘int’ to ‘char’ [-Wnarrowing]
931 | static char end_float[4] = {0x02, 0x00, 0x80, 0x7F};
| ^
entry.cpp:933:39: error: narrowing conversion of ‘128’ from ‘int’ to ‘char’ [-Wnarrowing]
933 | static char end_int2[2] = {0x01, 0x80};
| ^
entry.cpp:934:51: error: narrowing conversion of ‘128’ from ‘int’ to ‘char’ [-Wnarrowing]
934 | static char end_int3[4] = {0x01, 0x00, 0x00, 0x80};
| ^
make[1]: *** [Makefile:50: entry.o] Error 1
make[1]: Leaving directory '/home/slma/SeqMule/exe/vcftools/cpp'
/bin/sh: 3: cd: can't cd to perl
make: *** [Makefile:28: install] Error 2
!!!!!!!!!!!!!!!!!!!!!!!!!
ERROR: Failed to make vcftools

would you please help? Thanks a lot!

[kaichop]

It seems to be a compilation problem. You can use the docker image instead.

…

On Wed, Nov 23, 2022 at 10:26 PM slma2021 ***@***.***> wrote: I now can install SeqMule but it said I missed some programs, such as vcftools ry.cpp: In member function ‘void entry::make_typed_float_vector(std::vector&, const string&, int)’: entry.cpp:594:43: error: narrowing conversion of ‘128’ from ‘int’ to ‘char’ [-Wnarrowing] 594 | char missing[4] = {0x01, 0x00, 0x80, 0x7F}; | ^ entry.cpp:595:39: error: narrowing conversion of ‘128’ from ‘int’ to ‘char’ [-Wnarrowing] 595 | char end[4] = {0x02, 0x00, 0x80, 0x7F}; | ^ entry.cpp: In member function ‘void entry::make_typed_float_vector(std::vector&, const std::vector<std::__cxx11::basic_string >&, int)’: entry.cpp:657:43: error: narrowing conversion of ‘128’ from ‘int’ to ‘char’ [-Wnarrowing] 657 | char missing[4] = {0x01, 0x00, 0x80, 0x7F}; | ^ entry.cpp:658:39: error: narrowing conversion of ‘128’ from ‘int’ to ‘char’ [-Wnarrowing] 658 | char end[4] = {0x02, 0x00, 0x80, 0x7F}; | ^ entry.cpp: In member function ‘bool entry::check_missing(unsigned int, unsigned int, const std::vector&)’: entry.cpp:872:56: error: narrowing conversion of ‘128’ from ‘int’ to ‘char’ [-Wnarrowing] 872 | static char missing_float[4] = {0x01, 0x00, 0x80, 0x7F}; | ^ entry.cpp:874:43: error: narrowing conversion of ‘128’ from ‘int’ to ‘char’ [-Wnarrowing] 874 | static char missing_int2[2] = {0x00, 0x80}; | ^ entry.cpp:875:55: error: narrowing conversion of ‘128’ from ‘int’ to ‘char’ [-Wnarrowing] 875 | static char missing_int3[4] = {0x00, 0x00, 0x00, 0x80}; | ^ entry.cpp: In member function ‘bool entry::check_end(unsigned int, unsigned int, const std::vector&)’: entry.cpp:931:52: error: narrowing conversion of ‘128’ from ‘int’ to ‘char’ [-Wnarrowing] 931 | static char end_float[4] = {0x02, 0x00, 0x80, 0x7F}; | ^ entry.cpp:933:39: error: narrowing conversion of ‘128’ from ‘int’ to ‘char’ [-Wnarrowing] 933 | static char end_int2[2] = {0x01, 0x80}; | ^ entry.cpp:934:51: error: narrowing conversion of ‘128’ from ‘int’ to ‘char’ [-Wnarrowing] 934 | static char end_int3[4] = {0x01, 0x00, 0x00, 0x80}; | ^ make[1]: *** [Makefile:50: entry.o] Error 1 make[1]: Leaving directory '/home/slma/SeqMule/exe/vcftools/cpp' /bin/sh: 3: cd: can't cd to perl make: *** [Makefile:28: install] Error 2 !!!!!!!!!!!!!!!!!!!!!!!!! ERROR: Failed to make vcftools would you please help? Thanks a lot! — Reply to this email directly, view it on GitHub <#188 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABNG3OCBOZXFCXWY7DQVHO3WJ3N7NANCNFSM6AAAAAASBXOSDI> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[slma2021]

Thanks Kai Wang!
can you tell me how to use docker image?

[slma2021]

I think I got the docker image by pulling it.
however, I don't know how to run it

I found from web sth like
docker run -it broadinstitute/gatk:4.1.3.0

so i type docker run -it genomicslab/seqmule
but there is no response

please tell me how to proceed, many thanks!

[yunfeiguo]

Hi @slma2021 please check out https://docker-curriculum.com/ for a docker tutorial. I tested docker run -it genomicslab/seqmule on my end and it is working (docker version 20.10.12).